What motherboard components can I safely conformally coat and will this prevent condensation damage?
You can use a high viscosity liquid coating and selectively pour it on.
You can also use a low viscosity spray coating and spray it on like paint.
Most of the coatings have an UV tracer to check coverage.
Things to avoid are obvious, the socket and connectors. Less obvious are heatsinks, since painting those would be insulating them.
Also when you remove heatinsks you shouldn't coat thermal interface surfaces.
And do not underestimate the capillary action of the coating! Under the socket/dimm slots for example.
It it unclear what you want to do with the system, but I'd recommend looking for a passive cooled sealed unit, this ibase ags100 for example.
I think, in overall price, you'll be in the same range.

The coating has a small effect on package to ambient thermals for normal components or traces. Poor (too thick) spray application may change the impedance or even fail in high voltage tests due to poor dying/capturing moisture. Spray coatings protect against high humidity, pour coatings also provide mechanical rigidity.