It depends rather a lot on the model, actually. Quite a few out there are sophisticated enough to cope with the constituency system and correct for that to allow for local variations. One rather obvious way to see this is that in exactly none of the predictions ever did UKIP's ~10% or so of the vote translate into a predicted 65 seats, but rather somewhere between 0 and 5. Which is hardly a percentage-based prediction, clearly.
I do think the key factor is that polls can only work effectively if they are decoupled from the system they are trying to measure. Anything else you can correct for or try to account for, with some margin of error of course. Indeed, much of it already has been! As an example, it's been observed that typically Labour support ends up a little overestimated, for various reasons -- as a result, I'm fairly sure that the raw data gives Labour more support than is actually quoted in the published result (by about two or three points, say).
This is anyway going to take a more complicated fix than anything you or I can come up with, and isn't as basic as suddenly realising that we don't have PR in this country. I mean, duh.