I have to say, I'm with willing, building and managing your vault is a great aspect of the war: will I salvage poisons or bone walls from death?
With this system, the decisions war is almost build on (like the one above) are completely eliminated. Especially salvaging from a mono deck will become a lot less fun (hmm, will I take 6 entropy cards, or 6 entropy cards, as opposed to: will I take 2 discords and 4 antimatter, or do I take some nova's too).
For the auditing, it isn't that difficult, only time consuming, especially when one person has to do it all on his own. That can be easily fixed by taking 3 or 4 war masters (one for dd's role, and 2 or 3 to do the auditing), which will reduce the pressure on the audit-masters.
Also, it shouldn't be that hard to make a spreadsheet that compares vaults with decks to see what cards there are left, and what cards are overused (actually, I have a spreadsheet like that, and the only times we failed in deck building, are the times last minute edits were done which I couldn't recheck with my spreadsheet).
I can image an excel spreadsheet to do the same for salvaging (basically, substracting the vaults of different round, and comparing those with salvaging discarding, or, even better, using the sheet to do the camparing too (might be easier with deckcodes in SDPC, see team water section (when it opens))).
Anyways, I don't see really big problems with the current system, apart from human errors. The only human errors that could be eliminated is the vault updating, by giving the vault spreadsheet the SDPC input, and have the spreadsheet update the vault.