Mate the consensus for flamed or spalts is to tread easy in all aspects. I've a flamed top LP going at the moment and I've skim coated that in ebony timbermate. It has popped the flame but basically pooped the whiter parts of the maple.
Not sure what it would do on the spalt, but I'd recommend you steer clear of filling it.

Mine was always going to be a cliche stripped down LP done in solid black so my muddy looking flamed top is no tearjerker. The kit was a custom order that was supposed to have been solid mahogany, no veneer, but factory made a boo boo. I'll post some pics later in the build thread so you can see what I mean.