Having some experience in this process the short answer is yes, baking it caused the grief. Lawuer by nature is virtually NEVER dry. It dries and shrinks for years. Hence the reason it is so repairable. The problem is in fact that this process occurs. When you bake it, the Urethane clear kicks, and seals off, then the solvents in the laquer want to escape and have no path to do that, ESPECIALLY on a solid wood model like a speed plane. On a built up plane the solvents can find an escape path through the fuse or wing and out the leadouts etc. Still baking is not a good idea.
Of course, there is another option, that being that after every layer of differing material, you go bake it. so you build up the substrate of laquer, then bake it, do the glass , then bake it, color coats , bake it, clear, and bake it. Were it me, and I felt it neccessary, I would start with a bake cycle of say 150 degrees, then for each step, cut the temp by 10 degrees . In composites this is how Post curing is done. you bake it to a temp higher than it will see in its real life and then it is stabilized for any temp under that.
Now for the clears, spot clears are really no different than overall clears after a period of 24 hours or so. The real attribute to spot and repair clears is that they tack off faster. IOW, they are dust free much sooner than overall clears and this allows the painter to cycle cars through the booth faster, ( or in most cases these jobs are painted on the floor or under a prep station where dust intrusion is a problem)
Baking doesnt really create a stronger finish long term it pretty much just accelerates the reaching of that point. Its a chemical reaction and as long as all chemicals are together in the proper balance, it is going to cure to the same hardness.
I dont really like to bake clear unless its a deadline thing personally. I dont like to reduce my window to polish that way. For those who havent, rubbing and polishing urethane clears is best accomplished after about 24 hours, and before 36 to 48 hours has passed.