Here’s my understanding about 18th century shirts:
In the 18th century a man wore his shirt or a woman wore her shift just about continuously. The shirt was a combination of undergarment and sleeping garment and had many practical uses. And, remember, they wore no under pants, so removing one’s shirt meant stripping naked. A man could even work ONLY in his shirt, with the tails tied between his legs. In the subsequent novels, there are scenes where Jamie is working in his shirt alone, or Claire is working in her shift alone. An example of a time in this series where Jamie might have been working in his shirt only is in Episode 2, Castle Leoch. In the flashback where Jamie is telling Claire about the Red Coats coming to his home, he’s pitching hay — hot, dirty work; he might have taken his kilt off for this work. (For narrative reasons — we wouldn’t have wanted Jamie dragged off by the Red Coats just clad in his shirt — Jamie’s wearing his kilt, too.)
So, this is a long way of saying that his shirt is the LAST garment Jamie would have removed, not the first. In fact, if Claire hadn’t asked him to take off his shirt, he most likely wouldn’t have done so at all. In Episode 7 (and even more so in the book) Jamie is surprised, though agreeable, when she says she wants to look at him.
In regard to alix’s comment, for Jamie to have removed his kilt earlier in the scene would have been comparable to a contemporary man stripping naked. So, no, the kilt had to stay on until Claire initiated “things”.