I tried looking at the buffs in your tool, but it isn't catching it.
Yes, the Entity validation tool can't catch everything. There are too many nuances for that. However, if you find a scenario that you think could have been caught please open an issue on the tool's website (plus kharma given too for doing it). I'll see if it's something that can be validated or not in the tool if you help out like this.
http://code.google.com/p/soaseplugin/issues/list
The developer exe doesn't necessarily warn of all things too. For example the buffInstantActionType "MakeDead" does not work with AlwaysPerform. It does however work with OnDelay. My tool doesn't currently catch this and the developer exe doesn't seem to care too much either.
Also, I've noticed two "errors" that work fine in game: changing the damage type for a weapon to "AFFECTS_ONLY_HULL" and setting a passive weapon applied buff to "GAUSS" At first I was worried that this meant that the game wouldn't accept it, but it turned out fine- I figure this is because the original files don't make use of these values, but they work perfectly in game, as per my previous mod. This correlates with another "error" involving the "SpawnShipsAtPlanet" ability but does not explain the tool's bizarre attitude towards planet files and the .constants file: in the case of the former it freaks out with values (concerning the planetary ring effect or something to that effect) I never touched, though I did mod other parts of the files, and in the latter case it catches on the unmodded section of the file that was added to slow fighter build rates in combat. It also didn't catch any errors in the .constants file I modded for another project, which I found to be an issue with the engine.
Is this about my tool or the dev exe. I validate every release against the Diplomacy/Entrenchment/Vanilla files prior to releasing. If you want to send me the files, I'll take a look if it concerns the entity validation tool.
I think I fixed the issue with the passive weapon type for GAUSS, I believe it was excluded from the list of constants in the earlier version.