I had a 4.3 as well, and on my LS swap I chose to leave the frame mounts in place and use the "forward mount" adapter plate geometry instead of moving the frame side mounts (partially to hopefully allow a low mount AC compressor in the future, but I think I've determined to go aftermarket high mount instead). I don't think there's any drawback to it, just a little quirk when doing something non-typical. And in my view, having something non-typical is better than doing a bunch of work and buying new parts just to look more like the other guys, as long as there isn't a valid reason that it is wrong vs right.
As for the heater box, I'd look and see if you can modify or get different valve covers to gain the clearance. Or if you really mean "AC box" and you don't need AC, try to find a heat only panel that has much more room. Another option is to fiberglass in a notch as needed in a factory HVAC box. This is a common foul point on LS swaps because the block is shorter back there, and the coil packs mount on top of the valve covers. You have a unique situation of having interference on an SBC, but the problem is common with others and can share a common solution...
And I take it that your accessories clear even being ~1" farther back? Power Steering pump/pulley hitting the steering box would be the closest contact point, I would guess? Again, similar issue with LS swaps, and usually a smaller PS pulley does the trick.
If it was easy, it wouldn't be hot rodding