Can the Onix SP3 be used with a pre-amplifier?

Might be a little late for you, but I run my SP3 with a preamp in front (see system) with no problems to report.

It's not just putting two gain controls, but, unless the Onix only has a "passive" preamp section, or the preamp you want to add is itself passive...you would have two gain circuits in line. This I believe is more problematic than simply two "controls", which I take to mean pots...

You should be able to connect the output of the preamp with one of the two pair of inputs on the SP3 and then use whatever combination of volume controls on the preamp and the SP3 sounds best. You're putting two gain controls in line with the signal but there's no reason that shouldn't work.