I've done two tile jobs in the house. First was a bathroom, and I had a problem with grout and one tile coming loose, and it was due to lippage, and not enough mud on the tile. I ended up busting it out and got it reseated and grouted without issue. Used 1/4" backer board mudded/screwed down to the tounge-groove subfloor and mudded/taped the seams. The walls were a giant pain, I used Redguard as my waterproofing, painted four coats, horizontal, vertical and both diagonals. It's held up well for the 6 years since I did it.
The 2nd tile job was just a floor in the foyer. Spent more time cutting tile than anything else as I laid it in a diamond pattern. Have one area of lippage I can feel, its one of the highest traffic areas of the house, and has held up just fine for 4+ years.
Getting ready to do the kitchen, and I'm more worried about it than anything I've done before. Part of me wants to lay some thin marine or pressure treated plywood down on the subfloor, before I put down backer board, and even use some self-leveling compound before I set the tile. I plan on using Redguard around the sink/dishwasher area, and where the fridge is moving to, including the areas where the backsplash (tile) is going. Laundry closet is right off the kitchen, and thinking of extending the floor into there, and doing the same waterproofing there.
Our subfloor is tongue-groove lumber, and is about 2" thick. I don't anticipate this is a problem like the OP's?