I agree with you that a custom abutment is a superior way of restoring an implant. Personally, it is the only way I do it.
There is a great article from Heitz-Mayfield et al, "Clin Oral Impl Res 2020,31:397-403" called Implant Disease Risk Assessment IDRA- a tool for preventing peri-implant disease. I've gone over it with our hygienists (Perio office),and it enables them to quickly assess how things could go south for a patient. It has a graph that looks like a spider web, and many categories that put a patient at risk of peri-implantitis. One of those categories is RM-Bone, which is Restorative Margin to Bone distance. When it is less than 1.5mm, they are at high risk/red area, when it is more than 1.5mm they are in the moderate or yellow area, and when the restorative margin is at tissue level they are in the green or no risk zone.
In the references there is a great peri-implantitis study from sweden (paid by the swedish government, giving the researchers true freedom of science, and no pressure of any implant company) Derks 2016, Journal of Dental Research, "Effectiveness of Implant Therapy Analyzed in a Swedish Population", It followed 588 patients, over a 9 year period.
From page 47 "Patients with periodontitis and with 4 or more implants, as well as implants of certain brands and prosthetic therapy performed by general practitioners, exhibited higher Odds Ratio for moderate/severe peri-implantitis. Similarly higher Odds Ratios were identified for implants installed in the mandible and with crown restoration margins positioned at 1.5mm or closer from the crestal bone at baseline. "
Warning: Personal Opinion below..
From my limited experience and in my opinion, there is a better biological environment when tissue is in contact with sterile/clean titanium, than when there is any kind of ceramics close to bone/connective tissue.
I frequently see, when removing healing abutments (which please tell your doctors to only use a new healing abutment) small spots of bleeding, which come from ripping off the hemidesmosomal attachment from the tissues to the clean titanium surface(no odors noted),suggesting a better barrier from the oral environments than that seen when removing a crown on a ti-base (odors frequently noted).
If you think of the "cement gap" setting you are all using, as tight as it might be, 20microns is plenty for bacteria to colonize. There will be some microscopically rough cement at that crown/abutment interface. Wouldn't it be nicer to have that 3-4mm away from bone? just food for thought.
Some general practitioners might dismiss an article that shows if a general dentist is delivering the case the risk of peri-implantitis is higher, but I hope you will all find a nicer way of presenting the idea to your doctors than hitting them straight with data & science.
-Luis Guzman. Prosthodontist/Board Certified Periodontist/Amateur digital technician