The compilation time IS an issue, but could be worked around in SOME cases by using tiny builds-- still, when you're ready to put out a final release, that might require several trial runs with minor tweaks as errors crop up in the final compilation of everything together. (Not to mention the RAM usage..)
While I believe that EVENTUALLY they'll probably end up in one binary together, that's likely to only happen when the impact to actually compiling the thing is less to the developers.
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Try checking the MAME manual at http://docs.mamedev.org
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