Well, the Trek is modern geometry, so a 54cm may fit, but the 4cm "oversquare" sizing makes me think that frame is made for your size after all, as a 58cm reach on a 54cm seat tube is pretty elongated. The only thing I can say on that frame is make sure the seat post is high enough, and yoiu may have issues with minimum insertion limits there, but I don't know.
The LeTour seems a lot taller than you need, and I notice it's 5cm "undersquare," while your Trek is 4cm "oversquare." This seems like a huge difference in bike geometries for the same rider.
By comparison, the Cilo is a "square" 56cm. It feels smaller because it's shorter.
Fit can be all over the map. I'd be willing to bet a square 58cm classic bike would fit you fine, give you plenty of range for adjusting the seat and stem.
My opinion is the LeTour is too big, and way too undersquare to fit most folks. It's best owner would be one with long legs, shorter torso.
My opininion is the Trek reach is probably about right, since you're not complaining about back, shoulders, arms. If your knees bother you, check the seat height and where it sits on the seat post. On many modern bikes, if you get that fit correct on the "back end," you'll be fine. My modern bike frame is 10cm in height shorter than two of my other bike frames, but it can easily be made to fit, and does.
My opininion is the Cilo would be right if it were 58x58; and classic bikes, if they feel "too small," they generally are. I've not been successful using longer stems and seat posts on them, though logic says I should be. I get caught up in a pretty bike that's too small, try to make it fit, and it doesn't.
And knee pain has lots of causes. Fit first, then ride a bit. Then, see if your pedals are close to the crank arms. Those spindle extenders can make a world of difference, and so does the way your cleats are mounted, if you're using clipless. I have a couple of friends who buy SPD's because they can get a long spindle on certain models of pedal, and they say their knees can definitely tell.
Another issue is float. If you have no flexibility in the pedal/shoe connection, that can also cause some knee pain. For a tri, I use "no float" cleats, basically locking my shoes to the pedals with no movement whatsoever. For a long ride, I use cleats that move a bit, and pedals with some variable float.
That's what I think, right now, at this given moment in time. Good luck to you. I envy that 56cm Cilo, which is my size.