It's hard to tell what the culprit was, though some type of caterpillar (likely the hornworms you saw, unless they were still very small) is likely. Or, there were spots of fungal or bacterial decay that then created an opening which desiccated around the edges as it sunk in (which appears to be the case in the third photo, although it's not in focus).

Bt only works on young caterpillars (make sure it's a strain labeled for caterpillars and not flies or beetles), because the older they get, the more resistant they become to the effects of the Bt toxin in their gut. Some caterpillars are very hard to find or may only feed at night, so you could try inspecting the plants after dark to see if you can identify the culprit. If you think caterpillars are still present (especially if you see frass/droppings), though, re-apply the Bt as directed on the label to maintain protection, since it may wear off quickly.  For older caterpillars, a more effective ingredient is spinosad, although the product needs to be labeled for use on plants, and verify if can be applied directly to fruits or not. The kaolin clay (Surround) is more broad-spectrum and should discourage chewing insects in general, but it too requires regular re-application, though perhaps less often when it's not raining.

Miri

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Spinosad is translaminar in action, which means it can absorb into the leaf surfaces it's sprayed on but isn't truly systemic, so it doesn't travel to other parts of the plant. Some of the spray may stay on the surface as well, but don't mix pesticides unless each product specifically says it can be combined with another, or else efficacy could be reduced or plant tissue damage could occur. (Or, for edible plants, a combination might not be safe to use on harvested crops.)

Definitely avoid spraying flowers (which, for a presumed pest of the fruits, would not be necessary anyway), and yes, an evening or early-morning application can help to avoid bee exposure. There is no "best way" per se to apply it; you'll need to follow all label directions. Each formulation can have different instructions based on its ingredient mix (active ingredient as well as inert ingredients). Note, though, that any spray won't be very effective once larvae enter the fruit, so in that sense, a Bt, spinosad, or kaolin clay application will effectively only be topical since larvae would have to chew through a treated surface layer in order to be exposed.

This might be the work of tomato fruitworm, as you noted. Hornworm frass and leaf chewing signs can be hard to detect until the caterpillars are surprisingly well into development, but since you have experience dealing with that species, we presume that's not the issue here, then. Yellow-striped Armyworms have been known to chew into tomato fruits as well, and if we've ruled out the other two caterpillar species, that might be your culprit. Penn State notes that "they can have multiple generations per year and various overlapping stages (egg, larvae, adult) throughout the growing season."

Miri

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You're welcome.