Is there a real shift in balance if Blueprints players violate their blueprint?
Well, obviously if you can place your die on any of the 6 spaces of the card, even the filled-in ones, then of course you can always place your die. No re-roll needed.

However, a blueprints card usually has 3 or 4 spaces where you can place your die. I played this game many times and it never happened that we had to re-roll a new die. The only way this could happen is if you have high numbers on your card and ALL the remaining dice have smaller numbers. This is unlikely. But of course, if all players agree to purposely go for the highest numbers first, this might happen. But I don't see why you would do this. Even if glass dice with high numbers are available, the numbers are usually not so important for the other colors.

Thematic point of view

I know this game might be considered an abstract game, but do not forget there is a theme. You are an architect. You cannot build wherever you want. The filled-in spaces represent roads, other buildings and so on. You are restricted by the surroundings. You should respect that, otherwise nobody will hire you as an architect.

Technical point of view

I think the differences are very small. One thing I can think of is:
- it is slightly easier to have more connections for the orange dice (which gives point according to adjacent neighbours). With the official rule, you might have an orange die on the first layer next to a filled-in space and therefore you cannot use this space to have an orange neighbour and score more points. You will have to manage it by putting a die over the first one.

On some rare occasions you will be able to play a die that you would not if you follow the official rules. So, I think this makes the game slightly easier, but not by much.

But it also makes the game less interesting: what is the point of the blueprints if you can put your die where you want?

My experience with this game is: usually you tend to respect your blueprint (6 points is always nice to have), the only time when you don't is when you really cannot or when you go for "the tower" (all dice stacked together).