Just had my white oak 6" rift and quarter floors refinished (living room only due to too much furniture) and it feels rough to touch like sand paper. When I feel my dining room floors which were not refinished yet, it's super smooth where my fingers glide through. The knots in my dining room when I use a pen tip, it doesn't go through, but with the finished floors the pen tip goes into the knots. Just seems like it wasn’t sealed?

Water based bona HD traffic in satin was used. My wood floor installer is claiming because I refinished it, it's now more "rough" which I find hard to believe. He sanded it, did 1 coat waited 30 mins, did a second coat. Second day he came back did a light sand and did a third coat. First day approx 4 hours of work second day only 1-1.5 hr

Is it normal for it to feel rough after being refinished with 3 coats?

Water based finish soaks into the wood and swells any fuzz left from sanding. It is tough so the light sanding between coats don't always smooth the surface since it doesn't powder like other solvent based finishes to become smooth.
Since the sealer is hard, I use two coats of sealer before the finish. The screening will cut the grain raise a little better, then. Then you need to use heavy coats of the finish to cover any roughness. I think 2 coats of finish, after the two sealers is the way to go with water based finish. Seal is less expensive than the finish, too.
You can always apply another coat of finish, after buffing with a screen.