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I had a zoom call with the S-series product manager at UltiMaker today.
He said there's are two good reasons why they don't ship the S3 and S5 with a flex plate:
1. UltiMaker's bed leveling procedure involves "hot probing," to ensure that filament residue on the nozzle doesn't mess up the measurements. This hot tip, pressing into the PEX coating on the Wham Bam, can damage the coating (make a divot in it). I also heard from the CEO of Wham Bam today, and he's aware of this potential issue with hot probing. Obviously, there's no danger of a hot tip damaging a glass plate.
2. UltiMaker want 99.99% "press PRINT and it always works" reliability on the full spectrum of materials that they officially support. They've found that existing flex beds (like Wham Bam) don't work 100% perfectly with their full list of supported materials. For example, heavily warping materials sometimes "warp" the flex bed up with the material. Other materials have adhesion problems. Thus, they err on the side of "printing correctly every time" and sacrifice "easy removal" on the altar of reliable, versatile printing. Their market niche is reliability.
And I must admit that tiny-base, tall parts often get "knocked' off the Wham Bam bed for me on the FlashForge. Thus, I'm in the habit of using a raft every time for smaller parts. I'm guessing that the glass bed on the UltiMaker S3 will be more reliable in this regard (small parts will stick so well than they won't need a raft).
Their logic is sound to me, and I think they've made the right decision from a wide-spectrum reliability point of view. UltiMaker doesn't want to adopt a new technique if it's not up to their reliability and versatility standards, and I respect that. Making a flexible build plate that works perfectly is an open problem.
I will keep an eye out for "hot probing" problems on my Wham Bam surface. I do plan to keep one glass plate as plain glass, so I can test both.