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.

Wayne, Thanks for replying. 1) I was adding another circuit to the main panel later in the day of my original posting, so I checked the heater circuit. It was 5kW, not the 3kW I originally posted, but it's in addition to the heating element installed as part of the HVAC (probably wasn't clear in my original post)... the cost was $100 if I had the extra circuit installed by the time they put in the main HVAC unit, so I said "why not". This is the circuit I think I can now do away with as it's not needed with the new pellet stove keeping us warm. The "standard" heating element in the HVAC is now the "emergency" element, if you will. 2) So you're suggesting bringing a short main panel circuit outside to the transfer switch, thereby allowing for a single long run from the switch to the subpanel. Hmmm, that idea has a lot of merit. I would definitely want to go with an ATS, then, so I don't have to walk outside to swap things out (and shoveling snow to get to that side of the house... like the 4' we had in 3 days last year :( ). 3) I'll read it after posting this... 4) I was thinking of a Kohler or a Cummins-Onan, though I hear Kohler is often more expensive in the long run because they do their best to force you into using their own guys for general service. In that case, Cummins-Onan has a serious edge.

Gas is the way to go, you can't do it yourself but if you put to many dryers on that service you'll keep blowing the main or the only thing that will work at one time is the dryer, don't forget there will be washers running too, and lights, and you said it's in the basement of your house so everything else in the house that is normally on will be running also, that includes your heater and hot water and AC. Also have you talk to your local AHJ to see if what your planning is even legal it sound a little sketchy.

I suggest you try a medical forum (perhaps one that deals with alternative facts). There's nothing we can do to help with your neuroses in an electrical forum. The PANEL is not going to be a source: 1. It's pretty well shielded. 2. It's a small radiating area. The issue is the wiring. These are almost always unshielded in most areas (type NM or the like) and they are long and provide a much bigger radiating area (especially necessary when you're talking something extremely low frequency like household current). Any electrician can tell you the coupling/radiation from a long wire is pretty easily detectible. Inside a panel (even with the cover off) not so much. So if you are really in a panic, use metal conduit or MC cabling.