Seeing the pics, looks like you have things drying as best they can. I think water likely did come in the baggage door, if only one latch was secured. Water leaks are hard to diagnose, as water travels quickly after entry. With things still open on the inside will help determine point of entry, with more rain on the way.
My wiper seals do go down well past the slide floor, but assemblies vary. An Artic Fox is generally considered a brand of good build quality. The wiper in pic does look torn to me. I use a seal conditioner on my seals and wipers to keep them pliable. I also put powder on a sock, rub on wipers, after conditioner dries, to make the wipers slide with less friction.
Can't say, as to need for Darco replacement before retracting slide. Generally less friction is best. All are not the same, but if yours is on rollers, rather than sliding on a wedge, it may not matter??
Hopefully someone with experience, with similar brand/model, can better advise.
Water issues are frustrating, hope you get it under control.
Jerry