By that reasoning, Western Europe has been a "protectorate" of the USA since 1945 until at least 1991.
Talk about American Exceptionalism!
I wouldn't entirely disagree, there are a few caviates however. The western European bases are a contribution to an alliance network, and from what I've been able to ascertain, are funded by the US government - in contrast, the US bases in the Okonawa/Ryukuan Archiapeligo are partially funded by the Japanese government (40% at least reckoning).
You wouldn't be the first to think that western Europe is a protectorate, it is a genuine political movement both in the UK and US (and probably elsewhere) to remove them. (see Bill Maher for example).
Western attempts to subvert Japan since their first contacts in the 16th century could never get past
Japanese insularity. The Japanese had to be most suspicious of the British since they were the greatest threat. Japan was open (after considerable hand-wringing) to opening economic doors, not political ones. Japan enjoyed a degree of unity by the 19th century that the likes of India and the peoples of Africa and China could only dream of. The idea of handing over large tracts of sacred Japanese soil to
gaijin or their Japanese traitor puppets was unthinkable. But replacing the God-Emperor of Japan by declaring Victoria Japan's Empress
would be manyfold exponentially more impossible than that.
1) If they were so insular, they may not have been aware that Britain was the greatest threat, the Dutch and Portugese may have been there interacting longer, and could be seen as a more threatening presence - just a possibility, we haven't seen anything about Japanese attitudes regarding specifically Britain in this thread beyond typical stereotypes.
2) We aren't talking about "Handing over large tracts", that makes it sound like they were at all willing. A military conquest/occupation of Satsuma isn't at all "willing". However, having Japanese Daiymo/Shogunate sponsored by the British is entirely different. Each Daiymo could be considered a protectorate, and as such still control their territory in Japan, and the Shogunate would still control Japan.
3) Yes, displacing the Emperor would be unusual, and there is every chance that a British-sponsored Shogunate could well betray Britain, and chase them out, but they still wouldn't want an Emperor who would inspire pro-Imperial sentiments, having a unchallengeable, but not directly ruling, Emperor ensures a Shogunate system. As was mentioned, this could be simply a British Ezo Republic (but in Kyushu), or the same writ large. Not that we'll have them drinking Pale Ale and Gin by the end of the week!