It will help. Reducing disc size limits your winding space and number of turns and makes things difficult all round.
You can compensate to some extent by using higher grade magnets so that you can use less turns without having to use thinner wire. You may need to go better than N42.
Everyone has their own ideas but personally I would far prefer decent plain discs over awkward brake discs and if buying then it may depend on your disc cost compared with the cost of higher grade magnets. I regard N30 as dead and probably now you can get N42 at the same cost but going to N48/50 may work out more than decent discs.
I think you are pushing things to build a 10ft machine with those rectangular magnets and try for smaller discs. You may have to accept a reduced output and make adjustments to the furling to keep it safe. As long as you are prepared for this it will be ok. You will have to go through the test coil thing to get your number of turns if you want best results.
Flux