I see your point. You're absolutely correct about the more intelligent charging and lower gauge wire.
I'd still recommend avoiding the solar charge controller though. I think something like a VSR would be more appropriate. If you get the right one, it can perform your isolation functions, charge control and cranking battery control. Having a charge controller where you limit your current in order to avoid larger cabling will mean that you get resistive losses going down through the controller, being less efficient and wasting energy in the form of heat.
Whilst drawing anything from a battery connected to a charge controlled commutator, you can assume the battery is simply a node. Current draw through the battery will be matched by a power input from the commutator, so you're still going to be drawing from the alternator.
You can simply run off the batteries as their own power sources, and then charge them at a constant rate, like drawing from a water tank which is being filled by a thin outlet float valve, but even true deep cycle batteries don't love being fully discharged. They certainly handle is better than a cranking battery, but if you let it discharge regularly (which a 2/4 KVA inverter will easily do when running decent power tools) you'll wreck your batteries. A 30 amp controller will be equivalent to a 360 VA supply. Depending on the capacity of your deep cycle batteries, you could wear them down fairly quickly if you were using things like welders, compressors, angle grinders, circular saws, etc...
I'm not trying to be a bummer. I've just done a lot of this stuff before, and I've had a lot of things not work in the past. They're expensive lessons. I just wanted to give you some things to think about before you spend your money.