So I committed what many may think is a Cardinal Sin.
I drilled a drain hole underneath the driver's seat. To prevent rust, I sealed around it with the same sealant I used when I installed a roof rack on my work van. I then installed a drain tube from a 911 headlight bucket. It makes it harder for water to splash in from underneath. I got the idea from another post and if I can find it I'll give the OP credit. It's part number 911.631.259.02
I had to use a 1/2" drill bit. I never like drilling holes anywhere on a car, and this was no exception, but I can now rest easy that if I get caught in a rainstorm, my Immobilizer is protected. Flooding is not a concern in my area, but even it if is, water would have other ways of getting in.
Yes, I could have gone with ECUDoctors waterproof case, but somehow I'm not convinced by it. Plus, $150 for a plastic box seems like price gouging to me.
I'm thinking of drilling another hole in the front floor pan, but I couldn't find a good low spot that didn't have anything in the way underneath. Still pondering that one, and I have time since the carpet isn't dry yet.
Here's the hole with the sealant:
Here's the hole with the drain tube:
Here's a pic from underneath:
And here's what the drain tube looks like:
P.S.
I found the post that suggested the drain tubes. Thank you to old911doc: