The values used for funits/em are multiples of 2 because computers work faster with binary maths. You can use 4096 or 8192 if you like. You can also use funits/em values of 1,000 or whatever if you prefer. With modern PCs it is hardly likely to affect the rendering speed of your fonts.
Format, Settings, Metrics, Maximum, Calculate will ensure that no glyphs extend beyond the WinAscent and WinDescent, which is what leads to glyphs being cropped. This will happen in other applications too, so it is vital to design all glyphs within the WinAscent and WinDescent guidelnes.
See the FAQ thread at the top of the Support forum for some diagrams illustrating the various font metrics and terms.
I design my fonts so that WinAscent - WinDescent = 2458 or 2048 x 1.2
This gives a default line-spacing of 12 points for 10 point text.
Pali Regular:
WinAscent = 1907
WinDescent = -551
Garava
WinAscent = 1991
WinDescent = -467