Map size is a difficult choice, but I would concentrate on choosing an area where combat actually took place- no point in spending umpteen hours of work on detailing an area which was a backwater and won't see any action. If I were doing a Philippines map, I'd probably leave Palawan out, for instance. The most important areas are Luzon, Leyte and Mindanao, but you'd probably have to make two separate maps, perhaps even three for a 1:1 map, unless a Bright Spark manages to discover how to remove the IL2 engine's size limit.
I have already looked at a Borneo map, but given IL2's map size limit plus Microdem's restriction on DEM size, this needs at least two maps to cover KNIL activities- possibly three: one for West Borneo activities (KNIL air attacks from Singkawang II against Japanese invasion convoys for Miri and Kuching) and one, though probably two, North/East Borneo maps to cover KNIL air attacks from Samarinda II against invasion convoys for Miri, Tarakan and Balikpapan plus air defence of Tarakan.
Map scale choice is YOUR call- YOU are making the map.
I think when you choose to make a 1:2 or 1:3 scale map, you have to lower terrain in map_H in order to keep a good ratio between distances and heights.
That's what I did with Philippines by lowering luminosity in map_H.
I don't know the good ratio, is it - 50% for a 1:2 scale map, - 66% for 1:3 ???
I'm not sure, so I made it... upon my taste...