Hai,
Deposition rates of about 10 nm per minute and controlling the temperature of
the substrate to room temperature will help to get rather flat thin film of Al
on quartz. Oil free vacuum and moderate temperature to maintain stream line flow
of Al to quartz will definetly improve the film quality.. Using all this you
should be able to get RMS roughness of the order of about 2-5 nm with reduced
number of pinholes and almost no micro-bumps on surface.

If you are not looking for specific application of Al thin film then Al(1%Ti)
will also be  a good option to improve the things.

regards,
Pradeep Sharma.