That's what will happen and it will work out for everyone involved. Someone else said it before about there being a special group of starters recently that might have skewed our perspective.... Kershaw, Verlander, Scherzer. Those guys are rare and Skubal, odds are, won't join them. He could. But that's a risk you have to evaluate.
If money were no concern and they were willing to pay it, and it didn't cost them anything except money, then sure, sign him, be sentimental about it, ride it out, let him go into the HOF and be a franchise player who will get a statue. But if signing him means they now have some kind of restraints going forward then don't. I don't want a repeat of the mid 2010's where our deals meant we had to sacrifice roster flexibility and moves because of dead contracts.