Jefferies' designs looked like they were well thought out as credible pieces of machinery. The TAS designs don't exhibit that---they were drawn just to look different.
That said I think I've been able to make the scoutship look reasonably credible and not too much of a deviation from TOS' Starfleet design. I also tried to resist making it too sleek and well integrated. I hoped I could get a touch of ungainliness in it that would give it some measure of utilitarianism to its look.
When I look at the heavy lander I see something of an aircraft fuselage in it as well as something almost bug like. It certainly deviates from TOS' Starfleet look, but we can also assume that tech and hardware within a "real" Trek universe would have variations in appearance. One could rationalize that Starfleet engineers might not have designed the lander and that they contracted out it to someone else or purchased an existing design adapted to their specific needs.
I think the aquashuttle is going to be the hardest to adapt. I actually don't like the onscreen version at all and there's absolutely nothing aquatic about its appearance. But I'll make an effort to do what I can to adapt it to something remotely believable.
I made an effort once to draw orthos of the TAS designs almost exactly as they were presented onscreen. They looked ridiculous with horrible lines and proportions and, of course, way off scale and oversized. The scoutship and lander would make a DS9 runabout look small and at the scale they're shown it would be impossible for crew to get in and out of the craft without some form of ladder or mechanical aid, perhaps like those vehicles with stairs to disembark from aircraft seen at airports where you disembark on the tarmac. The main reason I don't accept the onscreen scale/size of the designs is best shown by how wildly out of scale the hangar deck is shown---it's impossibly oversized to ever fit in the ship we are well familiar with. So what we see onscreen in TAS is a very exaggerated style of artwork. And even the exterior of the Enterprise,
while immediately recognizable, is way off in how aspects of it were drawn.