Unfortunately no. In vanilla, you cannot place a blueprint over an entity to upgrade or rotate it. I tried it with upgrading assembly machine 2 to 3 and rotation an electric drill. Both of these don't work in vanilla with blueprints: you cannot place a blueprint with a differently rotated electric miner to rotate the existing one for example.
You can, however, place an electric drill over an existing one to rotate it "manually" (from hand - not from blueprint). Same with upgrading an assembler. But I'm not going to add this behavior to blueprints because I feel like it is out of scope for this mod.
If there is another mod that does that, I will make this mod compatible by inserting modules in that case. And if there isn't, maybe I will create one :)
Also, fun fact: you can rotate assemblers that have fluid input with blueprints. It is kind of weird, I will take a closer look at it sometime.