Ah gotcha. I thought you were talking about booting into Win98 and then opening a DOS window or something. I wouldn't worry about the 'difference' between what you are asking. The only thing I would not be sure about it memory managers...like himem or emm386. I'm not sure if those program are even necessary nowadays....haven't twiddled in pure dos for a while.
Anyways, regarding performance and stuff, basically, if I put together a new computer, say a 2 gig AMD system, and then load it with pure DOS and run DOS Mame, I will not get as good as performance as I would if I ran Win98 or 2000 with win version of Mame.
And vice versa, if I had a slow computer like yours (no offense) and I loaded up Win98 or 2000 and ran Win Mame, I would not get as good as performance as I would if I just did pure DOS.
Hopefully that will help you out.