So I can see why 'Twilight' might be a highly-favored episode by viewers in general, without implying they are in the A/T camp.
For all the grousing and negativity I hear about reset button episodes - people really seem to like them and respond to them. Yesterday's Enterprise, The Visitor and Twilight are all very beloved episodes for the narrative tension they create. They have to opportunity to show the characters in much different and darker circumstances that is normal for Trek. Also, the characters get to do things that would not allow the main story continue.
For all the talk of Twilight being an Archer episode, T'Pol and Phlox both show they are willing to sacrifice their own lives for a better future at the end - and they are both characters that could have escaped to their home worlds. This is assuming they did not realize that the Xindi/sphere builders would eventually destroy them. Archer sacrifices himself, but humans have nothing to lose at that point. And your point is very well-taken that T'Pol's loyalty to Archer can be taken outside of any romantic context - and actually plays better if she is acting out of friendship/honor debt rather than romantic love.
And I do think it is on topic to discuss Twilight in this thread, since Twilight created an alternative timeline or Canon AU for writers to work with. As for the A/T implications, I think I resolved them by the end of my story Dusk - so I feel free to love that episode without reservation now.