It's apples and oranges, really. What sounds better is really subjective.
If by better you mean cleaner, crisper and clearer, then of course a Sega Mega Drive/Genesis sound chip emulation on a computer will be better.
But if you want better as in more organic, authentic, genuine and closer to the slightly unpredictable noisyness of the real hardware, then you won't get that from Deflemask. Having something that sounds good in Deflemask is one thing, but it will almost certainly sound different on the real hardware and this is part of the fun of making this type of chipmusic. 
For that sound you need to use real hardware or another good way to get that on your computer is to use something like the Plogue chipsynth MD VST which literally emulates the noise and filters and actual electrical behaviour of the sound hardware.
