I've had my bike for a few months now. It's a Dawes Horizon; my first ever road bike. It fits well and I've never had any discomfort with it. I use it daily for my commute to work -- a journey that varies from several miles over rough track, to a journey of a few short miles up and down a very steep hill.
Despite the lack of discomfort, I'm always playing with the handlebar and saddle height, 'just to see'. Also, what feels like a good configuration at the end of the week doesn't always have the 'glove fit' at the beginning of the week (and vice versa). I'm not sure if that has anything to do with sitting down at a desk all day.
I had the bike set up perfectly the other week (the best it had ever felt), but I tweaked the saddle height too much and now I can't remember how it was configured.
So I decided to follow a step-by-step guide. I followed this one. But one part has me confused -- 'Tip 5, Handlebar Reach'. It explains that whilst riding on the drops, the handlebars should obscure my view of the front hub. Is that right? The way I'm seated, I have a very clear view of the front hub when I'm on the drops. I have the largest frame the bike's available in, and I'm only six foot -- surely the bike's not too small for me?
Could it be due the geometry of my bike? Is it different for racers?
The whole "obscuring the front hub" thing is a rule of thumb, much like "knee over pedal axle". It works for some people, it might not work for you. If you are comfortable in the drops, then it doesn't really matter whether or not the hub is obscured.
The rule was meant as a guide to stem length. If you raise the handlebars, they also get closer to you and so the effective stem length is shortened. If you lower them, they get further away from you.
If it seems to fit well, then you shouldn't care about whether or not you can see the front hub.
My suggestion would be that when you are adjusting saddle height and handlebar height/reach, only adjust one at a time. That way, if something feels off, you will know which to adjust. Adjusting both at the same time can be confusing. Set the saddle first, both the height and fore/aft. Then work on the bars.