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A counseling is just a piece of paper, it means nothing and holds no power. It's not a recommendation for UCMJ, it's not the initiation of a bar or a flag, or anything else. It doesn't matter what you write on there, it will go into a little brown folder that will sit in someone's desk and be shredded once the Soldier is gone. Only the commander can initiate any punitive action and your commander is not choosing to do that. Don't overthink how to write the counseling, just write it. You'll be writing another half dozen before Christmas.

Don't let turds take up all your time and energy. In time they all wash themselves out one way or another. Two weeks after they are gone the platoon won't even remember they existed. Focus your energy on doing good for your platoon instead of wasting time on the turds. You have a finite amount of time and energy. Prioritize it towards building your team up

Here's my current perception of the system.

The Army gives way more chances than soldiers need.

Do not be the one to give more chances. Situations like these, when completely unravel are going to burn the lowest level of rubber stamp authority Chain of Command that didn't execute corrective action according to the regulations.

The bigger problem now is the soldier has a documented paper trail that is auditable with negative leave. This cannot be swept under the rug within your ability to do so, and neither your company commander can just fix it, and will probably get the attention above battalion.

I SAY THIS because as a financial analyst by profession.............. If I were crunching numbers for higher levels of management a NEGATIVE DATA VALUE in the data column of Leave Days while in the bigger picture is very immaterial forces one to look into it because those numbers should never be negative.

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LEARN THIS!!!!!!!!!!!!! There are administrative things in the military that get tracked in systems that no level of military authority can fiddle with. PAY and LEAVE, etc... is one of those things without a very documented process to make those changes.

With however you go forward in your leadership in the Army don't presume kicking the can down the road can go on forever. Or maybe not. Maybe it gets totally ignored, and you get lucky. If it doesn't though you're going to get a solid lesson in bureaucracy and covering your ass.

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That LAST THING you want is a problem soldier to continue to be a known problem soldier to the command and then end up doing something that injures or damages property that causes a General to take action.

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Finally, start keeping folders in your computer with all actions, communications and documentation regarding this soldier. It will be handy when things are investigated.

It's all good fun until someone gets seriously injured or killed and the line of duty investigation reveals the blatant disregard for policy.
Saw something similar at Fort Sill, late 90s, SQD LDR , PSG and PL rendered false reports to cover a troops absence. Soldier was found dead in a stream bed. Guess what happened..... Yup ,reliefs all around.

My two cents; do what the commander told you as far as counseling. Additionally make damn sure you report the troop as absent on any daily admin reports. Publicly report the troop as absent during PT, work call and any other formations where a report is rendered.