So there's no question that the CD (Windows) version is faster overall, but here's a short list of the speed differences I've found between them:

Faster on CD:
• The Neptune's movement (marginally)
• Text loads automatically
• Clicking skips through data capsules and supply station outros

Faster on DOS:
• Center positioning skips most problem triggers
• Fewer overall problem triggers
• Hammerhead 1 (V) midpoint spawn is further forward, skipping a problem

Undetermined:
• Question content/frequency appears to be the same
• Load times between scenes seems different, but no consistent pattern yet

The biggest change is the CD version patched the center position skip, which means there are more questions that are unavoidable. Although it does save some time because you don't have to worry about setting up to dive through a problem.
e.g. The first problem in Dragon Reef 3 (V) can be skipped, but is slow to maneuver around the hitbox. In CD, it's faster to move straight through it.

The next biggest change is now that problems are so much faster to clear, it's possible some may be faster to get wrong twice and move forward (if it's not an obvious answer), and some death warps are actually slower.
e.g. The first problem in Fossil Trench 1 (V) can't be skipped, and may take a few seconds to answer. Because Zoom is nearby, it's possible to just tank the problem and refill in the next room.

Along with a few new problems that pop up, the level strats are sometimes significantly different. Also without long delays during problems and combos, you don't get much rest time and no free time to calculate a problem while it loads. Just something to keep in mind if you plan on playing on that version. So far, it the CD version saves about a minute per zone.