Polytetrafluoroethylene (PTFE) is one of the best-known and widely applied PFAS commonly described as persistent organic pollutants or "forever chemicals".
If I want to avoid PFAS due to environmental concerns, is there an alternative to:
None of those items are needed.
If you have a bowden extruder, upgrade to a direct drive.
Even on direct drive systems, PTFE tube is commonly used as a "reverse bowden" or "feed tube" to deliver the filament from a drybox or spool mounting point to the toolhead. Other tube materials may be used, but may contribute too much friction; you'll have to experiment if you want to go that path. You can usually forgo having one at all if youu mound the spool with a good direct path, or setup a system of filament guides/pulleys.
If you have a PTFE-lined hotend, replace it with an all-metal one.
Direct drive extruders may have a small piece of PTFE between the extruder and hotend, even when the hotend is all-metal. This part of the filament path being low-friction is not critical, and it can be replaced with a 2mm ID metal or even printed plastic tube without seriously compromising extrusion capability.
Nozzles should never be PTFE-coated. Don't buy ones that are. The best nozzles are 100% tungsten carbide (never wears out, never wears into air or into your printed parts), but pretty much no nozzle should contain any PTFE unless explicitly marketed as such (eew).
As a lubricant, there are lots of choices other than PTFE sprays, most of which are probably better. PTFE is highly recommended against for linear rails, as it's reported to lead to sliding by the balls instead of rolling. For smooth rods it might be a good choice, but I would expect there are grease, graphite, or other options that work just as well. I've never used a printer with smooth rods so I can't recommend anything in particular from experience.
It depends on your printer really. If you have a direct drive printer with all metal hotend, then you can feed filament directly into the carriage without any guiding tubes.
For example, the Prusa i3 models (MK3, MK3.9, MK4) don't require any tubes, as shown in Prusa's own promotional photos:
Edit: It seems this is misleading marketing, as there is apparently ~5cm of PTFE internal to the carriage.
As for replacing a Bowden tube with something other than PTFE... I don't know any of concrete examples of a proven solution, but really any tube in which you can easily slide your filaments (i.e. low friction) will do.
If you are printing PLA and PETG I would expect you can get away with using Polyurethane ("TPU"), but might need to lower your speeds to overcome the friction. I've not tried any, but I can see that if you are in the US (I'm not) you can get a variety of soft (i.e. flexible) tubing from McMaster-Carr
The inner diameter may differ slightly from the usual PTFE tubes the printers come with, in which case you may need to tune retractions (larger inner diameter -> more retraction needed).
If you have an all metal hotend, then the Bowden tube itself won't be subject to high temperatures, so the important characteristics will be its inner diameter, whether it can flex the way you need for your particular printer, and if filament can be pushed through it with relatively little resistance.
If you are feeling adventurous, you could even try printing your own tube from TPU and see if the idea can work at all. I'd use some of the stiffer filament, perhaps with a shore hardness of 98A which when printed solid is about as tough as shopping trolly wheels. If you print it thin it bends quite easily.
