I'm looking to get the Trek Domane 4.3 and debating between a size 54 and a 56. One shop I've been to told me I'm a 56 and another said 54. According to Trek's sizing chart I'm 56. I am 5 9" with an inseam of 30.5". Which is the right size for me? Btw, I prefer not to replace any parts or make modifications to the out of the box setup. It should also be noted that I prefer comfort over performance.
There are a ton of info online!
for example: http://www.ebicycles.com/bicycle-tools/frame-sizer
Performance usually mean right size and also same comes for comfort. I don't know why you think that this things are in opposite ways.
If you feel like 56 is too big and 54 too small go for the smaller. Also what use you will give to it ? Smaller frames are better for more aggressive driving like in a urban enviroment.
I know some cases when in a store seller advised wrongly in order to remove some last year(o more) stok. So be careful with this. It may happen in some small stores where the seller is also the owner.
Go through this process. It will ask you to measure several body dimensions and will help you pick the right size frame by how long it is rather than where the toptube meets seattube, which makes a lot more sense when you think about it. It will therefore work the same with a road vs a crossbike (which tends to have lower top tubes) and any compact or other frame designs. You can look up the geometry chart for the model you are interested in to find the Virtual / Effective Top Tube Length and pick the one closest to your optimum.
If you are between two frame sizes I recommend choosing the larger one. It is easy to use a shorter stem than what it comes with and should your goals / flexibility change in the future you may appreciate being able to go to a longer stem (if you ever want to lower your handlebars you may also want them further away).