what you've discovered is what most competent bike shop guys already know:
you can't fit a bike just by the numbers, and you can't fit a bike alone.
there are just far too many variables:
1. you have a two-inch range of inseam sizes. which one is correct?
2. what kind of flexibility do you have in your back? in your pelvis? in your knees? this is a big one, since it will help to determine your reach, the headtube length, whether you like steep or relaxed angles, and your handlebar drop.
3. do you have proportionally long thighs or shins? what is the crank length on the bike you're trying?
4. how is the size of the bike measured? to the centre of the top-tube or to the top of the seattube collar?
i'll give you my own experience. i have been riding a 50 cm marinoni leggero with a 52.75 cm tt [measured to the centre of the tt; it's about 52.5 cm to the collar], 170 mm cranks and a 4 cm handlebar drop. the stem is 120 mm, the seatpost has a 2.5 mm setback and the saddle is pretty far back on the rails. the bike fits perfectly, and i've been riding it for five years.
i recently bought a litespeed teramo. it has a sloping tt [i have proportionally shortish legs] and in the medium size [a "virtual" 53 cm], it has a 54 cm tt. i went with 172.5mm cranks this time [long thighs]. it fits me perfectly with a 100 mm stem and a 4 cm drop. my saddle is in the middle of the rails on the 2.5 cm setback seatpost.
so... how could this be? how could i feel just as comfortable on the litespeed with a longer tt and a 64 cm reach as on my marinoni with a shorter tt and a 64.74 reach?
well... there are differences... the marinoni has a 74 degree seat angle and a 71.6 degree head angle. the litespeed has a 73.5 degree seat tube and a 73 degree headtube. the headtube lengths are about the same. and then there are those cranks... and they have different saddles that give slightly different pelvis and leg positions...
the point is that there are so many variables to consider. the vertical frame size and top tube length are important considerations. but they're a starting point. the important thing is to find a bike that you can be fitted on, and then remember all of the metrics of the perfect fit. if this is your first road bike, i can understand the frustrtion and confusion. the best i can say is "be patient" and only use online fit calculators as a starting point.