Just like when people merge mine Namecoin the nmc blocks aren't included in the btc blocks.
The merged-mine implementations that don't include the memory fix: (mutable vs imutable storage) and no auxpow data in cblockindex (blocks stored in memory) will eat up alot of RAM... so far only Devcoin and I0coin are the ones that have this fix and only Devcoin is running on 0.9.2 (currently in testing) with all the other fixes that bitcoin rolled up along the way included. So for most of these incompatible alt-coins who now wish to merge-mine (because I called that they would, and the ones that dont will die) are now suffering from either memory bloat issues or incorrect implementions/bugs and its next to impossible for a general programmer to port it over because its increasingly convoluted code to keep track of.
which is exactly why i've been warning everyone about these leech coins or sidechains that wish to piggyback themselves onto the Bitcoin mining network to secure themselves.