That's a lot to think about for sure. Guess that having never done a rebuild without removing the cranking shaft just never seemed to be an option, but, it could.The big fear would be the cracked main webs for most people. The question of disturbing the main bolts and possibly speeding up the demise. Setting aside options of lock-n-stitch, welding the cracks, using studs, balancing rotating assembly etc. as things to improve it- If you continue driving it you go with the theory of not disturbing as best option.
Ok- so if you tear an engine down to the point you remove the pistons and rods from the crankshaft. In a normal rebuild you would lastly remove the crankshaft. Simply don't. Wrap the crank with the lint free shop towels to keep it from scuffing when you use the ball hone on the cylinders and cleaning up flashings, etc. You are going to have to take extra care and wont get the benefits of balancing crank or new main bearings. You dont have the option to bore the cylinders and use bigger pistons. But SO WHAT? You weren’t going to get those benefits anyway if you don't do the partial rebuild.
The new rings will still do way better than old ones for the worn cylinders and a fresh crosshatching always helps. And now with new rod bearings, cam bearings- (people are afraid to do Cam bearings themselves-it is very easy- just a way machinists get to make more $) and new oil pump- even with worn main bearings the over all oil pressure goes up and flow improves. You can balance rod-piston assemblies and doing that helps. True best is crankshaft also, but the rod/piston balance is half the battle. You find issues like any lifters, rocker arms, rocker buttons, valve springs so weak they are beginning to float- that are close to failure and can catch them before they fail.
When you have the oil pump off, you need to use something to flush the main bearings well to ensure no contamination that may have gotten in while open doesn’t stay in the main bearings. Depending if 6.2, the rear main seal is harder to install with crank in place, but very doable. Other than that, the rest of the build will be basically the same.
There’s examples of 100% rebuilds, and some that go way beyond that making tons of improvements. Do what you can, and don’t let the “wish I could” or “while you’re there” hold you back from making improvements you can enjoy or get rewards from just because right now doesn’t allow the perfect rebuild.