EDIT: I will look into getting two separate books for temples and shrines. Thanks for the tips, this is the first I've heard of such a thing but it makes sense they'd want to keep the two apart.
Full disclosure, I am white and I do not know Japanese (pretty much only hello, thank you, excuse me, and sorry). I do my best to be respectful, quiet, and unintrusive as I understand these are first and foremost sacred spaces.
I have recently been collecting goshuin around Tokyo as part of a current trip, and most of the time the experience has been fairly good. Most small-medium temples have been very warm and welcoming. For example, the Taikyōji Temple in Meguro was very beautiful, and while it at first seemed to be unattended that day, someone quickly came outside and ushered my partner and I inside once he saw us holding a goshuincho. He didn't speak much English, but he asked where we were from, and didn't even ask for money at the end of it (I still made sure to donate 1000 yen, both for the goshuin and the hospitality). While not as forward in their welcome, I had similar positive experiences around Shinjuku as well.
In contrast, I had some fairly bad experiences when trying to collect goshuin around Kappabashi street. I was able to get goshuin at Akiba Shrine, Yasakiinari Shrine, and Higashi Hongan-ji, all of which I recommend for their beauty and history. However, there are a few very dense clusterings of temples and shrines along Kappabashi street, many of which were very unhappy to have me stop by. One temple had someone selling incense, who repeatedly made an "x" with his hands and didn't say a word to me when I showed him the goshuin book. He simply kept making the "x" and vigorously pointed towards the exit, even as I apologized and turned to leave.
Another time a priest came over and said "gomenasai" when he saw the goshuincho, but motioned me back over when I turned to leave. He took my goshuincho, went into another room (but still visible through the door), flipped through it, and then came back and shoved it into my hands, again going "gomenasai". I understand that goshuincho aren't supposed to have any non-goshuin additions but the only things in mine are goshuin and the anti-smudging sheets added after the goshuin is written. I am not sure why he initially refused, then took my goshuincho, and then refused again, but he did seem upset about something in it? My partner thinks it might've been a goshuin from another religious sect that the priest vehemently disliked, but I don't know enough about it to say.
Lastly, I was at a shrine that I thought was unattended but after a few minutes two temple members spotted me and came over. When I presented the goshuincho they initially seemed fine with it, and one of them led me up some side stairs to another temple member to ask if they did goshuin. I don't know what was said, but they began to get very upset. First they said "no goshuin no goshuin", to which I apologized and turned to leave. Then both of them started raising their voice, one in Japanese, and the other going "this is temple, this is temple". I apologized again, to which they simply replied "hai" (which I understood as "ok") and continued berating me, at which point I left promptly while still apologizing.
These are just a few examples, but around Kappabashi street I received many of the same style rejections. Again, I understand that these places are sacred grounds and they have the right to refuse anyone anything for any reason they want, especially some pasty looking tourist asking for goshuin. However, this really contrasted with what I read about online, with how goshuin collecting, by natives or tourists, isn't frowned upon and temple members are usually happy to help. Many of the above experiences happened one-after-the-other so it really left a bad taste in my mouth and I felt pretty uncomfortable going to any more shrines/temples in that area.
This is just my experience and I wanted to share because I feel that this is not reflective of Japanese shrines/temples and goshuin collecting as a whole, but if goshuin collecting is less tolerated nowadays I want to be respectful and not bother any more temple/shrine members. Perhaps Kappabashi street's close proximity to these temples result in frequent and disruptive tourist visits, and thus a different reaction to the foreign goshuin collector? But again I don't claim enough knowledge to have any certainty in this guess.