I am confused about bike fit. I am 6'1 and ride a 58cm Specialized Secteur Bike. I had a BG fit done and my stem shorted down to 90 mm to relieve some upper body back pain (originally 110) . The fit seemed to work. Recently I went to have a fit kit fitting done to explore having a steel touring bicycle built. I did the fit kit and learned I have about an 88cm pubic bone height and a lot of other measurement were taken.  After the fit, the bike fitter told me I had very short femur bones I think 16 inches or something like that . I was told I need a very steep seat tube angle to get my foot over the center of the peddle spindle. He suggested my present bike be modified with a zero offset seat tube and he moved my seat 2.5 cm forward and we added a 110 mm stem angled upward.

Ok I am very confused how does one bike fitter set me about 7cm aft of the bottom  (measuring bottom bracket through the center of the seat)bracket and another suggest a zero  offset tube and place  the saddle all the way forward.

I was told because of my short femur to get the ball of my foot over the spindle I need to bring my foot forward.  Still I could have sworn I had my foot over the spindle when the seat was back, and now have it over the spindle with the seat forward. The problem is I am pretty far forward on my bike now and it feels like I need to push my bars out even further.

I did some riding with the new position and got some pain on the lower outside of my left knee that I didn't have before. When I was on the fit kit machine it felt really great, but applied to my present bike it seems a bit weird. 

What confuses me more is I want the bike for touring. Is it normal to have a touring bike with a 75 degree seat angle? I guess I am sort of confused by bike fitting.