Mac users have 3 choices (or was it 4?) Glyph Designer is just one of them. There is also Hiero and bmGlyph... and one other I'm forgetting.
Windows users like me, only have one choice -- BMFont. I've never heard of anyone having issues with any of those exporting to NGUI, and Glyph Designer was used quite often. Yes, it sounds like you should export with the "match char height" option, assuming it will export the font properly. 64 pt font means jack, to put it bluntly. All fonts have different DPI, so 64 size in one font can be huge, and 64 size in another can be tiny.
Using pixel size is the only proper way to go, and BMFont forces it by default.