Image Capture works just like it always did. Turn off iCloud. Then that whole rigamarole of
upload the photos from my iPhone to iCloud, download them from iCloud to my Mac, run A Better Finder Attributes to correct the dates, and then run Exif Viewer on my iPhone to get the original file name (IMG_9999), and then use that info to manually change the names on the photo files.
becomes unnecessary. But here's a thing: you're confusing file dates and photo dates and they are not the same thing. You're trying to bend the Finder (a file manager) into a Photo manager. Photgraphs track the date of the image in Exif metadata. The file manager doesn't work with Exif. It's perfectly possible and legitimate to have a different file date from the photo date. That's one reason to use a photo manager.
How many files would I end up with?
It doesn't matter.
When the Photos.app takes my original photo, it is moving that original into it's multi-multi-multi file structure or does it make a copy (so that's 2 files).
It makes a copy. So the obvious thing is, after importing to the database you delete it from your own file structure. Going forward, as you import directly from your camera/phone, that step becomes unnecessary. So, one file.
Then it makes the thumbnail (3 files).
So what? You never see or meet that file. It's tiny. Takes negligible amounts of space. It's just a tool to help you browse your images quickly and easily.
When I export the original photo into a folder, does it remove all the other files or would I then have a total of 4 files?
Why would you export it? What purpose? Once it's fulfilled that purpose delete the exported copy. The master is still in Photos. See?
If I chose to delete the photo from the photo app, will it erase all the extraneous files or will I need to search for them manually to delete them?
If you delete a photo from Photos all the versions and thumbnails are deleted as well.
Consider the Contacts App. It's the front end for all your contacts and their details. You never see the database behind it. If you need an address or phone number, launch Contacts, search it and there it is. It shares the information to other apps like your email client. What goes on behind the scenes doesn't matter. If you want to add an address or change one you don't go looking for the DB behind the scenes, you launch Contacts and do it there.
Same with Photos. It's the front end for all your photographs. You never see the database behind it. If you want a photo you launch it and search. There's the photo. It can share the images to other apps without ever exporting - or you can export if you like. But what goes on behind the scenes doesn't matter. The number of files doesn't matter. It's all just a lot more simple than you think.