I’ve neer been an enormous fan of WHM, in the long run it pays to know what you are doing. Still it does have a very useful role to play, even if some of the things it does just seem plain strange. Yes EasyApache does give enormous flexibility, but so do the vendor provided packages.
Some days the only way to fix things is through SSH’ing into the server, and you have to be really careful to make sure that you don’t change something at the command line that WHM has it’s claws into.
suPHP seems to be the default handler (I can kind of understand why for multi-tenant hosting setups, but perhaps you should have a real sys-admin hired in that scenario?). It has a charming habit of doing the unexpected; todays head banging surprise came from wondering why php.ini settings were not getting applied.
After lots of grepping for ini-set statements, we eventually find an suPHP_config directive in .htaccess.
.htaccess has a lot to answer for, and if you are looking for real web performance you should _NEVER_ use .htaccess – put the configuration in the Apache configuration file where it belongs. The additional cycles Apache has to spend checking for the presence of .htaccess and parsing it if it is there will hurt you in the long run.
Allowing your “webmasters” to specify their own php.ini through .htaccess is just plain wrong.