what I don't get is why am I feeling this resistance while the clutch is in all the way?
Doesn't matter. You're clutch disc and input shaft still have inertia and have to be rev matched to the output shaft speed of the gear box. This is what your synchros do.
and I was always told that up shifting doesn't require rev matching for daily driving because the engine auto rev matches for you naturally.
Lol, not that kind of rev matching (engine to tranny). I'm talking rev matching your input to tranny output (sometimes known as double clutching, but not so important on up shifts as down shifts).
is that roughness normal? will it damage the transmission? can I counter it with a heavier shift knob for a slightly faster throw?
It's normal. No, putting a heavier throw on there will not work. Well, it might but I wouldn't recommend it. Your synchros are between the collars and gears in your transmission. When you go to shift they are squished and sandwiched in there so they will bring the gears to nearly the same speed through friction. Putting more pressure on the (like a heavy knob would do) and forcing them to do it harder and faster will wear them out faster.
Learn how your car wants to shift properly. My STI is happiest when I drive it a little more aggressively (i.e. don't beat on it but don't drive it like a granny aka I mode). Shifts are butter smooth then and the shifter practically pulls itself into each gear. No resistance.
If you haven't, you should read this article and learn about what's going on in your transmission. It'll make you a better driver for it. I've taught plenty of people how to drive stick (including my wife) and I always start with making them read this. By the time I'm done with them, they all know the concepts like double clutching, heel-toe, rev matching, engine braking, etc and perform them regularly.
HowStuffWorks "How Manual Transmissions Work"
Come back with more questions after and I'll happily answer them.
In reality, a lot of people don't recognize that you don't need to shift hard to be fast. Even shifting fast is all over-rated and it only for looking cool in a movie, or impress some people that don't have this common knowledge.
QFT. When I drive I shift with two to three fingers. Very light pressure. Now, WOT is of course a different story but every day driving is a very casual flick of the wrist. You'd be surprised how little energy it takes to shift the car when you do it right. Like I said above the shifter practically falls into gear on its own.