Given that Jeph always liked Tilly it was inevitable that we'd see them again after a while.
However, I admit that this particular wrinkle was completely out of left field. That said, we know that Station is anthroposexual (my term for AIs who are attracted to humans) and, in a lot of ways, Tilly's personality is very similar to Hannelore's with high levels of anxiety and hyperactivity and an overwhelming drive to help (although manifest in very different ways).
They are not dissimilar physical body types either. So, maybe it was inevitable that he would be attracted to them.
Here's a thought that occurred to me after I saw this strip on Patreon and noted the number of people wondering about the physical end of this relationship: Maybe, for them, it is entirely fulfilling enough to be with a mind that shares their goals and values them intensely on a personal level? Could they even be asexual? Of course, it's equally possible that they have had the brain implant that Hannelore didn't want and Tilly and Station are having hot, sweaty virtual sex every night; it's unlikely that Jeph will ever tell us unless there is some kind of joke there.
FWIW, though, I can see lots of sweet stuff happening. Things like Tilly lying in their bed and Station starts playing romantic music over the compartment's intercom, playing with the life support settings to add her favourite scent to the air and other things that are the unembodied AI's equivalent of hugging them all night.
Finally, about Station's panel 4 punchline: It's odd but, sometimes, characters in this strip become audience surrogates and I suddenly realise that Dr Ellicott-Chatham is this forum right now!
EDIT
Removed a sentence that isn't correct and that I'm worried will otherwise derail the discussion of my points about how the Stilly ship probably works.