These two videos from my favourite YouTube amp guy describe the issues he has with an area on an eyelet board on a modern reproduction of an old Fender amp, that's fairly conductive.
As he says, just because they used a material on a classic amp, doesn't mean it's still the best material to use.
I'd be wary of a varnish style spray as I have no idea whether it would improve or reduce the board resistance. Plus, around the eyelets, it's going to get hot and burn when you solder them, and the carbonisation certainly will reduce the resistance considerably.
I'd suggest if you want to carry on with the idea, you start with a simple test piece with a few eyelets in a group around 1cm apart, apply high DC across a couple (say 500v DC, so you'll need a suitable transformer and rectifier circuit to hand) and measure the DC voltages on nearby unused eyelets. Then repeat with your clear-coat spray on top and bottom and sides. Solder and desolder the eyelets a few times on each test piece to represent real-life usage and heating of the board and finish (e.g. you may find the eyelets become loose). Really no point progressing beyond any testing until you are certain the MDF is fit for purpose.
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