What problem am I missing if we just mask of the offending bits. For my own project which uses auxpow (and thus has weird nVersion), I also used the bitmasking method to get rid of auxpow version bits before making the standard integer comparisons to deploy BIP66 using IsSuperMajority():

    if ((block.nVersion & 0xff) >= 4 && CBlockIndex::IsSuperMajority(...)) { //...}