[Wayne A. Pflughaupt]

On the one hand I can see that by reducing the cut of the filter the electrical signal was in effect "boosted" thus it's working a bit harder, but only on certain frequencies...

Yup, reducing the cutting filter on the red one will have the same effect as boosting those frequencies. The net effect will be that the red sub sub will be working harder than the green one, because the green's level across that range remains depressed by the equalizer.

...and certainly still nowhere near as hard as it would be working without any EQ.

More oft than not, any equalizing places additional demands on a sub, both its amp and driver. Before equalizing, your operating sub level is determined by any peak in response that you might have (~43 Hz in your case). When you cut that peak, you now find that your sub is too quiet, so you have to turn it up to compensate. Naturally, that places more demands on the sub than before.

I guess my brain is having trouble wrapping around this question. Is it better to:
1.) Have an identical signal to both subs even if one is clearly dominant (4-8dB higher across most of the spectrum) and the other is only shoring up where the first is weak. *or*
2.) Have two individually flat subs that are within 2-3 dB of each other for the majority of the spectrum.
The red sub is still going to be lower than the green except where the green is weak, but the separation in strength would be much less, if that makes sense. But with the combined SPL mostly following the upper envelope, would it even matter?

See, already you're obsessing. You should have taken my advice to just stick a fork in it and sit back and enjoy.

But - as long as we're obsessing, it's best to simply try it both ways and see which you like better. Either way you do it, demand placed on one sub vs. the other will no longer be the same. You only get that with no equalization to either one (assuming you keep both their gain controls set the same).

But the main thing you're after by adding the second sub is additional headroom. You're still getting that no matter what.

Regards,
Wayne