getting the feeling that Nathan is more quoi than aro, but that he doesn't care that his feelings don't fit neatly into any categories, or that the good doctor's feelings aren't exactly the same as his, or that the doctor's very doting and affectionate towards all of his close friends and not just him. despite his mandatory jabs at Nathan's Summerset background, the doctor cares about him a tremendous deal. he enjoys and desires Nathan's company, and supports him wherever he's able to - unconditionally. and that's what matters!
Rafael, meanwhile, experiences both romantic and carnal yearning for the good doctor. both he and the doctor are aware of this, and it's not An Issue.
(if anything, the doctor finds it kind of alien but also cute, to Raf's slight mortification)