300-3 (b) "contained in the same raceway" etc. is mainly intended to prevent the hot and neutral, or hot and ground, from forming a loop that has a large area or contains a lot of iron. Those conditions increase the circuit inductance and could limit a fault current to a value that makes the breaker slow to trip, starting a fire somewhere before the trip. If the hot to the subpanel and the hot coming back for the circuit in question were in different conduits, and the neutrals did not run along with them in the same conduits as the hots, then there is a problem. If the hot to the subpanel and the hot coming back are in the same conduit, without the neutrals, then there is no technical problem, but the AHJ may not like it because it complicates the situation and could lead someone later to unknowingly create a problem. Code is whatever the AHJ says.

Even with gas heat, that's a lot of A/C you've got there, almost 110A worth on it's own. Did you do a proper load analysis? I've heard of outside panels in warm places, but the rather "tropical" nature of Louisiana makes me nervous. I won't screw with 30 circuit panels. What's the point. THe delta for 42 is small and you always have issues with spaces. There's tons of special circuits that need to be addressed. I recommend you get someone who has a clue about things draw up your electrical plans at least. You size breakers for the wire, NOT the other way around. WIre sizes depend on the type of wire, the ampacity required, and the length of the run. Larger feeders tend to be done with aluminum just for cost practicality. There's no problem with aluminum of feeders/services provided they are installed PROPERLY. You can wire everything with 12 G (that doesn't need more than 20A) if you like. Makes things more convenient, especially if you've got longer runs.

A number of companies make a combination unit that is a meter can and a small panel (8-12 spaces, 16 -24 circuits) that have feed through lugs. All you need to do is run the 4 wire feeder from the new panel to the old, and make sure the neutrals and grounds are separated (neutrals must be isolated from the box) at the old panel. Unless there is a local rule that requires a disconnect at the sub panel it isn't necessary. If the existing panel has a main breaker you can use that for the local disconnect if you want one, but the main breaker in the new feed through panel serves as the required service disconnect and overcurrent protection.

I was looking at wiring diagrams for prewired transfer switches and they do exactly what I want to do. Take the hot wire off the breaker and connect it to the transfer switch which contains a breaker but they leave the neutrals and grounds where they were. So are they also wrong? I am not aware of the derating current when using a conduit but I suppose it has to do with "back emf" or eddy currents. I will have less than 15 feet of conduit and thought it easier & neater than running 12 NM cables. However I can just run 12 black(hot), 12 white(neutral) & 12 green (ground) in my 1 1/4 conduit. Or are you suggesting 3 separate conduits for each type of run?