What does "你舒服吗" mean in a relationship context?
歪了歪了…… I can see why 你舒服吗 will be easily interpreted as sexually comfortable.

Because without any context, we will not use 舒服 to describe relaxation of mind. And extremely structurally simple sentences are often uttered in sexual intercourse...(Think about it.)

Avoiding using words that have ambiguous meanings like 舒服, however, is an option.

The best choice is applying both: longer, specific sentence &amp; proper words.

E.g.

我快要到了（I am about to arrive.）√

要来了（I'm coming...）x

你感到放松吗（Are you feeling relaxed?）√

你舒服吗？（emmm...）x

这椅子坐起来很安适呀（The armchair feels very comfortable to sit on）√

好舒服呀（Ah~Good~Yeah~）x