The senate is elected on a slower cycle, and simply by nature of its differing powers you might get different dynamics. You see that happen in some other democracies, at least.
Also: just because the senate should be proportionally scaled doesn't mean that proportionality needs to follow the same rules as the house's: e.g. one of them might use winner-takes-all per district approach, another a ranked choice, or one might use districts, and another be a proportional representation of the whole state.
Finally, while a slight variation in the representation is likely "nice to have" I don't actually think it's all that critical. The idea makes sense: you want a check on power, but in practice it fails at that goal today, because power is not wielded by senate vs. house, but instead by republicans vs. democrats (sure, in the exceptional curent case of a precisely divided senate where every vote counts there's a slight possibility that intra-party disagreements mean that some senators sometimes switch sides, but even now it's going to be rare). But it's really important to realize that the senate does not exercise any kind of legislative check on the house in the normal case that congress is either clearly divided or clearly in the same hands. When house and senate are in the same hands, it's the political party that makes the decisions and members generally stay in line; and conversely when it's divided it's the political parties that do the horse-trading. There's no protection or moderation offered by the current system; if anything it makes for even more extreme legislation - because now it's either deadlock or go!-go!-go! - and when congress is in gung-ho mode, they don't have the luxury of careful consideration, and so likely produce less moderate legislation.
The current split is a failure; not a feature.