(Ok, warning.. I'm gonna ramble. I tend to do this a lot. To get my point skim to the last paragraph.)
Mainly, that depends on which plane you want to model. Considering the accuracy of the 1/48 valks, there shouldn't be any problem making a VF-1, since they obviously work in real life, and look like they may fly.... although I'd hate to imagine the turbulence generated by the arms underneath.. not aerodynamic at all really. In fact, it's likely that most of these planes wouldn't really fly, without VERY advanced avionics systems to counteract the instability of the designs.
Anyway, getting the proportions correct can be a pain on some of them, especially the Mac+ ones.. They're very complex transformations, and although they can be done in real life, like the few transformable kits have proven, it's VERY hard to keep the proportions of one mode correct without fouling up the other modes. The fighter mode of the YF-19 is just beautiful in my opinion, but honestly, the Yamato 1/72 transforming version doesn't do the design justice. One of my friends commented that the fighter mode of the Yamato looked more like a bloated goose than an aircraft, and I could see what he meant. The intakes and rear fuselage are way too thick for the size of the plane. It looks very out of proportion in fighter mode to me... not at all like the Hasegawa fighter-mode model. Certain aspects of the aircraft had to be sacrificed to make a viable robot mode that would stand on its own. Now, on the other hand, I've seen people who converted the Hasegawa kit so that it DID transform.. I have no idea how. But I couldn't find pics of the battroid or gerwalk modes, so I can't tell you how they turned out. I could only tell because of the gaps between parts, and the places where hinges had been placed.
The main problem here is that these aircraft literally are not possible in our world. I'm guessing you've probably seen the way the wings of the YF-21 worked. They literally could change shape, almost like a bird's wing, which can change individual feathers to change its shape. If that wing can do that, I would assume that they could apply that technology to other parts of the aircraft, changing the shapes of various parts to fit together like an organic being, instead of a rigid metal airframe. This can't be done in real life obviously, but you can do it on the computer. In order to get the best proportions for all the modes, you may have to scale certain parts during the transformation.. in the case of the YF-19 you may need to shrink the nose and enlarge the head for it to appear correctly in battroid mode, after being in fighter mode. It's a balance.
To start off, modeling the separate parts is probably a good idea. The VF-1 is pretty blocky overall, and fits together simply, so it shouldn't be hard to get the parts to transform correctly. Starting in fighter mode is probably best, since that's where the fitting of the joints is crucial.. you can make the fuselage one piece, then break it later so it folds. The YF-19 is an entirely different story. I don't fully understand it's transformation to begin with, since I've never seen any examples. But the shape is so flawlessly smooth, it's difficult to tell where the joints are. You can see the lines for the joints, yes, but there's no physical break in the curvature of the surface. This thing demands you build it in one piece, then break it up later.. and that can be a problem, since the parts later have to all break apart, and turn into a correctly proportioned battroid. From the other end, if you build the model first as a correctly proportioned battroid, you might be up a creek when you attempt to fit the parts together to make the fighter. Sheesh, even the Yamato has that problem, with the joints and fuselage not coming together all the way. It's a big tradeoff that depends on what you want to do. If you want an accurate battroid, the plane probably won't fit together. If you build a nice fighter, the battroid may have a tiny head and limbs that don't look beefy enough.