Hate to say it, but there is a recognised Standover clearance that should be observed. I am a Shortie-30" inseam, and I can rarely get a frame to give me that clearance. I currently have a 15" Bianchi and a 42cm Giant. Both are compact frame design with long seat posts. Then to get the bars far enough away, I have to extend the stem. Standover height is a measurement that can be altered. Providing you have a clearance and the rest of the bike fits- I would not worry too much. Incidentally, even on the bianchi- I only have 1" clearance.
That sounds like your Giant is way too small. I have a 26" inseam, am 5'2" tall and ride a 44cm road bike with compact frame and a 37cm MTB. I have barely a cm clearance on the road bike, but it is just fine.