No dont do it the paint will act like a insulator and shorten the life of the motherboard... I'm pretty sure they still make motherboards that react under UV lights DFI had a few of those i'm sure..take a look at the manufacturers I,m sure someone still does
i gotta agree with jack rabbit and say go for it. if you can afford to kill whatever your working with, then why the hell not. at work we conformal coat entire PCB assemblies that go into high speed cameras among other things. now they have a lot of components that get hot. how hot? hotter than components on a motherboard? it's impossible to say, but all i can say is that a 1/8inch thick conformal coat on those bad boys doesn't cause any problems with them.
sounds like an interesting mod and certainly one that would reap impressive benefits if it turned out how i would imagine you are envisioning it. and as we all know...anything that turns out spectacular has a chance of flopping hard.
You could tape off certain parts that are going to create the most heat couldnt you? Then just peel the tape off after? I dont know lol Im sure everyone here thought it but figured it would take a newb like me to say it
__________________ "And thus I clothe my naked villany
With odd old ends stol'n out of holy writ,
And seem a saint, when most I play the devil."