How should a SM who is on Permanent Profile have their PT test graded for Promotion Points?

Are you talking a permanent profile or a temporary profile? If temporary then you simply don't take the PT test until you are off profile. If you are talking permanent profile then you perform the events that are listed in your profile. The most common profile is alternate aerobic event. in that case it would look like this

***FOR PROMOTION POINT PURPOSES ONLY***
Push Ups: 98%
Situ Ups: 100%
2.5 Mile walk: Pass

Total score: 297

Pass the alternate event and you get the average of the other events as your score for the alternate event.

***EDIT***

I just had time to get in the reg and this is what AR 600-8-19 has to offer.

"(1)Permanent profiles.
(a)Those Soldiers with permanent physical profiles for the sit-up and/or push-ups events will be granted 60 points
for each event waived and use the actual score for each event taken and must qualify on the 2–mile run or approved
alternate test according to FM 21–20.

(b)Effective 1 April 1995, Soldiers taking an alternate event for the 2–mile run and receiving a passing score
receive a score for that event equal to the average of the scores for the other two events.

(2)Temporary profiles.
(a)Soldiers with a temporary profile that prohibits taking one or more events of the APFT will use their current APFT score provided it is not more than 1 year old at the time of the promotion point computation and the Soldier was
not afforded the opportunity to take an APFT or an authorized alternate test.

Do I agree with the way it is done? No, not really, because I have always maxed my push-ups and done average on my sit-ups. This means that no matter how fast I walk my score has already been decided as long as I pass. Prior to my permanent profile my PT score averaged about 280-290, with a permanent profile my score is 250-270. So yes looking towards E-6s, I already have fewer promotion points. The current regulation does not inspire SMs with permanent profiles to put forth their best effort, that's for sure.

AR 600-8-19, Enlisted Promotions and Reductions will have the answer you are looking for. As for how it is done, it doesn't bother me. I do not worry about what other people are getting for points while on profile and such. Too often, we are worried about what someone else is getting. I focus on me. I focus on doing my three events and doing the best I can to get the best score possible. If I got upset about what I thought to be a percieved injustice by the Army, then I would spend my whole day whining about how someone has it easy or better. Continune to focus on your and don't worry about what somoene else thinks. They are not signing your paychecks nor helping you in your career.

Right now I have a permanent profile that will not allow me to perform any of the alternate aerobic events. I am in the Army Reserves and they averaged my push-ups and sit-ups which gave me a pretty good score. But I am not saying get on a permanent profile, but what I will say there's always ways for everything. And for promotion purposes I see each of your points. But we don't write the FMs or ARs we just abide by them .

SSG Houde--there is way too much emphasis on a physical test that does not really measure soldier fitness. Not many people would pass the real test of soldier fitness--can you run and carry a ruck, weapons, ammo, your buddy, etc? Can you defend yourself in hand to hand combat? Can you withstand the mental stress? And so on...so we come up with how far and fast you can run, and do things by age group. Wars are not fought that way, unless you consider old congressmen sending young men and women into harm's way. We need more training at the unit/squad level. And of course not all the staff and low density skills set fit. However, the Marines treat everyone as a rifleman first, which is a radical concept for the rest of the services.
Which leads us to the profile...and I had several permanent profiles toward the end of my career. I took PT tests anyway. I deployed anyway. For those who cannot, it is very silly to require a test. It is pointless unless the point is we just can have anyone "get over". Rounding out as you describe above also proves nothing. It supports a mentality that we are stuck on stupid. That does not mean we should not have PT. Nor that we should not have a test. Nor that we should be fat and lazy. Permanent profiles should be evaluated every year. If the doc says no test, no test. If you can run, you run. You should meet the standard for what ever you can do. What you cannot do should be trained until you can do it, if a doc says ok.

I don't 100% agree with the current system, but I don't have a solid recommendation to change it. I am on a permanent profile due to a foot injury, and post-exertion problems. Last time I did the APFT run I took 2 weeks to recover; however, I know that I would have a higher APFT score if I could do the run instead of the walk. Before my permanent profile my APFT average was 270+, and the APFT I took that required 2 weeks recovery I had a 291. Currently, my profile allows me to do the run or the swim as an alternate event. This wouldn't be an issue except my medical condition makes it much harder for me to do situps as well and this isn't waived (I still max push-ups). So taking the average of my push-up and sit-up scores significantly drops my APFT score. So my promotion points have dropped significantly due to my profile. I don't agree with this because the only reason I have a permanent profile is because of the medical condition I developed while deployed. In my opinion the Army is negating me for a condition directly related to my service. Fair? I feel that the Army should give me the option of a medical discharge/retirement if they are not (or cannot) treat me fairly when it comes to promotion.

The average between the two events should be the score for the event the Soldier did not take !

The policies you are looking for are FM 7-22, AR 600-8-19, and AR 350-1

I have seen it first hand and honestly I see no issue with it. While at WLC our female iron warrior was on a profile, some of the others complained about it, but honestly, I saw no issue with it at all. I have no doubt if she had been able to run she would have maxed that out too. When people are doing more than max on the other two events, or even just maxing the other two events, it stands to reason that they should be able to perform at the same level on the third. I feel like it just keeps them from getting screwed over in the long run. Most people I know on a permanent profile, and remember I said MOST, still work hard to excel at everything they can on the APFT.