A fecal transplant definitely doesn't work for celiac disease, which is the only gluten intolerance you have to worry about.
Other gluten intolerance is probably not gluten, gluten is just a close enough proxy. Could be FODMAP + IBS or maybe some other sensitivity.
Why are you narrowly focusing on gluten intolerance when this line of comments appears to be denying whether gut biome is worth caring about due to having impacts on health?
> Could be FODMAP + IBS or maybe some other sensitivity.
Seems extremely unlikely. Of someone is eliminating gluten they from their diet they usually aren't also eliminating dairy, legumes, and other high-fodmap foods; gluten-free is restrictive enough already.
The only other sensitivity I could think of in which this makes sense is wheat sensitivity (but not other gluten containing grains which are less common).