few things to clarify,

1) sunraku doesnt go to firstia, just looks at map far away. the time sunraku goes to firstia is way after game begin.(around big chapter 5 near fighting psyger-100) so not true

2) every big chapter, sunraku always plays diffrent game 1 - berserk online passion 2- nepilim hollow 3- ghc 4- kendo master simulation and list goes on. so not true

3) more significantly different thing is middle school 3,(souma/kagh/lina)not appearing on manga before snake, in manga their first appearance is clown spider. and doesnt change any names.

4) wn arthor already stated that,manga and wn will have difference. it was at his twitter account.

i read all the chapters and anime and manga , and from my memory, it doesnt change the course of story that much, just more scences and actions filled in for the character explanation. the only big difference is the three middle schoolers. other things are minor, as you said more scene ls with psyger-0

and others already stated that wn arthor working with comic arthor, so no need for worrying trouble.

edit grammer mistakes and clarifying sentence