Is there a reason you believe FreeDOS interrupt latency would be inferior to MS-DOS?
(I can certainly imagine virtual 8086 mode / emm386-style shenanigans, varying with configuration and what's loaded in your config.sys, but this is all very hypothetical, and the most straightforwardly hypothetical position of all is that one bare-bones 16-bit DOS should be exactly the same as another in this regard, not necessarily being in the loop at all.)
(I can certainly imagine virtual 8086 mode / emm386-style shenanigans, varying with configuration and what's loaded in your config.sys, but this is all very hypothetical, and the most straightforwardly hypothetical position of all is that one bare-bones 16-bit DOS should be exactly the same as another in this regard, not necessarily being in the loop at all.)