Certainly is a pain! One solution - bin all the lights and indicators and just have a brake light, that simplifies the lot. LED's are good and take up far less space too.
Indicators - ive' seen some very small, plastic / rubber ones in black that I will use (if I can find them again) and fit in the old rear mudguard holes - almost invisible as they blend with the frame.
Number plate is the hardest & may depend on your viw on legality (MOT plate vs smaller day to day plate). If the back end was higher you could tuck it behind your battery box & claim it as still visible from the rear.
Personally, I think the side mount looks clumsy & spoils the lines. I have a different seat - more flat-tracker - but will be going with a plate that just fits between the frame rails at the back...(I think it's 5x3). Looks lie your frame is modified though so not such an obvious fit, but you could still hang something smaller under the seat - keep it fairly horizontal so it's not too obvious.
Other option which holds it out of the way is to use a the 'German style' plastic found on lots of BMW trailbikes. This is designed to ensure the rear wheel isn't the last piece of the bike and you can mount the plate on that too. Means that the seat lines aren't affected.
