There are number of issues with bike fitting.

It's not just the leg extension.

The width of the bar in relationship to your shoulder width.
Seat width in relation to your pelvis width.
top tube length
height of stem in relationship to the seat...
amount of drop in the handlebar. Women specific handlebar have less of a drop than a "standard" handlebar.

As for riding on the hood:
either a fit, lack of core strength, lack of strength in arm and hands.

riding with hands on the drops:
again fit, lack of core strength, lack of strength in arm and hand and lack of flexibility.

there are many things that does affect your comfort.

You may have issue with flexibility. Warm up before a ride and stretch out.