Is it helpful for other chronic diseases? If so, how much and is it cost-effective?

I agree that there's lots of unanswered questions, and plenty of theories to test. But we do have lots of data suggesting that FMT would be very helpful for other chronic diseases (http://HumanMicrobiome.info/Intro, http://HumanMicrobiome.info/FMT, etc.). I’m trying to get us to the next stage of demonstrating that it can be highly effective in humans for numerous conditions. 

Regarding costs, I think cost-effectiveness is one area where FMT should shine. Stool is free, and currently has no value. The value derives from what the few extremely healthy people are willing to sell it for. The costs around FMT are mostly associated with finding donors, donor screening, storage, and shipping. I believe there have been a few papers looking at cost-effectiveness of FMT for C. diff, and finding it to be a good choice. https://www.ajmc.com/view/fmt-is-cost-effective-for-any-recurrent-clostridioides-difficile-infections-study-says 

I believe that costs can be lowered even further by switching from a stool bank model to a “direct from donor” model. Yes, there are some cons, but I believe they are outweighed by the pros. 

We started off selling a whole stool (10+ doses) for as little as $150. The only limitation was that we were unable to find the tiny percentage of “ideal donors”, for that price, and thus had to raise prices. We’re currently selling for $100 per dose, and doing means testing for low income people. I think this is plenty affordable, and most other sources of FMT are selling for 2-10x the price. Ultimately, it’s up to recipients/patients to determine if the costs are worth it. But so far, there are certainly many people willing to pay thousands of dollars (much more than we’re charging) merely for the potential to help their conditions. If FMT is demonstrated to be highly effective for many conditions, I have no doubt that people would be willing to pay tens of thousands for a high quality donor. 

Can it be safely administered at home? You make the claim that donation and use of FMT can happen outside of the hospital setting; this is currently not recommended.

Naturally the medical community would not recommend people to perform a medical procedure on their own without supervision. There is certainly some merit to that, and we do recommend that patients get medical oversight from their doctor. 

However, the actual procedure is extremely trivial (swallowing capsules, or performing an enema), and there is no need to have a doctor perform it. There are even downsides (delays, costs, colonoscopy risks, limited dosing, etc.) to having it performed as a medical procedure. 

The primary difficulties with FMT are finding & screening a donor. It would be nice if doctors were able and willing to order the testing, but there are some restrictions with that, and most/all of the testing can typically be ordered online. 

There is a growing literature around the effectivneess of autologous FMT (use of your own stool for transplantation) may be as effective as a donation from someone else (one paper I am aware of, but I am sure there are many more).

I would strongly disagree that autologous FMT has been shown to be similarly effective as FMT from a high quality donor. We have reports of 50% improvement for autism, and 90% of IBS patients improving. 

I do not think aFMT is logically or scientifically supported by the current gut microbiome and FMT science (including much of what was referenced in the OP). I have an FAQ page here that provides some commentary and citations on aFMT: http://HumanMicrobiome.info/FAQ

This quote from the aFMT paper you linked actually supports my donor-quality hypothesis:

the microbiome of a healthy individual can deviate from an ``anti-inflammatory” (healthy) state to that of ``inflammatory” state of dysbiosis

In so far as what they’re considering “healthy” donors are actually not healthy. And they actually have dysbiotic, unstable gut microbiomes. 

One of their other main arguments seems to be that an unhealthy gut microbiome (of the patient being treated) can sometimes be less dysbiotic. Yes, that’s certainly true. But I don’t think that supports using aFMT over FMT. An ideal donor should be much safer and more effective than using a “merely not sick”, or even a sick patient. 

Another one of their main arguments is the lack of difference some studies show between aFMT and FMT. Again, my opinion is that they are merely demonstrating that their “healthy” donors are actually non-ideal donors.