I've installed over a megawatt of PV panels and not seen any with aluminum wire. I've run several miles of PV wire and not seen any #10 or #12 that is aluminum.
You aren't supposed to hook more than 2 panels (or strings of panels) in parallel without over current protection to each string. So, just connecting 3 panels in parallel to bus bars or thru Y connectors isn't recommended.
Technically #12 isn't big enough for 3 panels in parallel. Solar arrays are considered "continuous" current by the NEC's definition so you have to multiply the Isc by 125%. You also have to multiply by another 125% to account for the fact that solar panels can put out more than their rated current under certain conditions. This means you really end up multiplying the Isc by 156%. This means your main wire down from the roof, with three panels, needs to be able to handle 29.67 amps. That means even #10 is barely large enough.
I would either replace your charge controller with an MPPT unit that allows you to run all 3 panels in series or upgrade your wire to at least #8 and put a fused combiner box on the roof.