I've found hardi backer to be better to work with. Comes with the bonus of having pre-defined spots for your screws that are a little below flush to the top of the board. That being said I've pretty much 100% gone to decoupling membranes - just way less work to roll out a mat of plastic and mortar it down vs. 3000 screws and cutting cement board. Also if you're picking cement board to add stiffness, you're better off adding plywood to your floor than trying to do it with cement board. More on reddit.com

I used Permabase and am very happy. But I am not familiar with the “permabase plus” you’re mentioning. I got mine at ISC Building materials rather than Lowe’s. More on reddit.com

Many professional tile setters still prefer cement board over newer products like Wedi Board or Kerdi Board for several reasons: Proven Track Record – Cement board has been used for decades and has a long history of success in tile installations, giving professionals confidence in its durability. Lower Cost – Cement board is significantly cheaper than foam-based boards like Wedi and Kerdi, making it a more economical choice for larger projects. Readily Available – Cement board is widely stocked at most home improvement stores and tile suppliers, making it easier to source quickly. Durability – It’s extremely tough and can withstand abuse during installation and construction, unlike foam boards, which can dent or crush if mishandled. Rigid and Stable – Cement board does not flex as much as foam boards, reducing the risk of tile or grout cracking due to movement. Fire Resistance – Unlike foam-based boards, cement board is non-combustible, making it a safer option for certain applications, such as behind a fireplace. Moisture Resistance with Proper Waterproofing – While cement board itself is not waterproof, when paired with a waterproofing membrane (like RedGard or Hydro Ban), it provides excellent moisture protection at a lower overall cost than waterproof foam boards. Better Adhesion for Thinset – Thinset mortar bonds extremely well to cement board, providing a strong base for tile installation without the need for additional primers or adhesives. No Special Fasteners Required – Cement board can be installed with standard cement board screws, whereas Wedi and Kerdi require proprietary washers and screws, adding to material costs. Familiar Installation Process – Many professionals are used to working with cement board and are comfortable with the techniques involved, avoiding the learning curve and potential mistakes that can come with newer materials. While Wedi and Kerdi boards have advantages (like being lightweight and inherently waterproof), cement board remains a go-to choice for many pros due to its affordability, durability, and reliability. More on reddit.com

the chances of them cracking the tile over years of use seems high enough to me that I'd probably want to do something about them. can you back them out and drive new ones in their place, sometimes the second time around you can get a better countersink. grinding/cutting them off would be better than nothing. More on reddit.com