He was never scheduled to go to Japan surely, as like Dunk and Groß he's having a post Euros break. Ever RDZ said this a few months ago, explaining why Rushworth would be key for pre season.
So the omissions seem to be:
Injured:
Verbruggen
Estupinan
March
Ferguson
Post Euro / Copa America holiday:
Dunk
McGill
Groß / Undav (possibly leaving)
Olympics:
Enciso
Likely to be sold/loaned:
Moder
Dahoud
Peupion
No idea.... Pedro
The Japanese Goal article says the travelling squad will be:
▽ Goalkeeper
23 Jason Steele
38 Killian Cahill
39 Carl Rushworth (additional decision)
62 Hugo Fischer (additional decision)
▽Defender
2 Tarik Lamptey
3 Igor Julio
4 Adam Webster
19 Valentin Barco
29 Jan Paul van Hecke
34 Joel...
This article says Joao Pedro is no longer going to Japan.
'Joao Pedro, who was originally included in the squad, has canceled his visit to Japan.'
https://www.goal.com/jp/%E3%83%8B%E3%83%A5%E3%83%BC%E3%82%B9/premierleague-japantour-add-member-20240719/blt8d7241cfcfab990c
I guess it depends on if we are absolutely sure Verbruggen will be back to playing in six weeks and there won't be any setbacks. After last season (Estupinan/Enciso spring to mind) we need to remember that return dates aren't always reliable.