Sure - I have subscribed to that thread, so no need to add further updates here.

I have had another look at Everydoor and now understand better what happened. I think there are really two issues here - the general one about amenity=fixme, and a more specific one about what happens if you change from fixme to a "real" shop type in the same edit. Maybe a more detailed description is helpful:

1. While surveying with EveryDoor I saw something that was clearly an unmapped shop, but it was closed for the night and I couldn't tell exactly what kind of shop. I searched for "shop" (maybe with shop=yes in mind) and chose "shop fixme" from the drop down list.
2. I now know that this immediately creates the 3 fixme tags (none of which refer to "shop", so the interface is a bit misleading).
3. While still editing the POI, I noticed that a website was displayed, which allowed me to identify it as a stationery shop. So I changed the shop type to stationery. 
4. I now know that this created shop=stationery but left the other 3 tags in place. I suppose I should have checked the raw tags at the time. I normally do that when changing the type of an existing POI in EveryDoor, in case there are tags that are no longer relevant to the new type. But in this case I was still in the process of creating the new POI so I didn't think of it.
5. Reviewing my own changes at home I spotted the fixme tag and removed it. I easily noticed the fixme:type tag also, as it is close to fixme in alphabetical order. But I simply never noticed the amenity tag. As I had not tagged any kind of amenity at any point, and was not aware of Everydoor using amenity=fixme on other POIs, it was not something I had in mind. 
6. Once that was done, there was nothing to attract my attention to the amenity=fixme tag, even though I look at POIs in this area quite frequently. So it stayed that way until you mentioned it.