See, we have different opinions as to what looks right. That's a good place to start. To me, a side mount looks out of balance and tends to suggest that the builder ran out of ideas or didn't think about practicalities until it was too late in the build. In reality, bikes look better without plates, but that's not an available option for most of us.
There are very few cases where the rear cannot be raised and I am yet to see a well designed seat and fender arrangement that precludes mounting a light and plate. On the Phat Trakka project, I have exactly that issue because I removed all of the rear fender and it has a seat that is not designed to take a light, but that's where it has to go.
The usual problem is that the seat is too close to the tire and/or the fender is removed, so the mounting is now too far forward.
If you could post a picture it might be easier for us to come up with some suggestions.