I don't know a heck of a lot about MySQL, but according to gmax's excellent New twist for DBD::mysql, DBD::mysql currently does emulate placeholders but in such a way as to preserve security. I'd suggest reading his node for further details.
As for LIMIT ?,?. The reason why it was not supported since 2.9002 is that it allowed for sql injection attacks, and it is not trivial to fix, in fact, I *just* scanned over Patrick's code and found a bug in the LIMIT handling code