They had no choice once Gunn took over and he decided to do his own thing. The Justice League cameo at the end of Season 1 is a different continuity than Gunn's. By keeping some of the stuff going they sort of mucked it up. Now, Justice League we have been watching is one universe. Suicide Squad he wanted to tie into his universe (including Peacemaker) which is a different universe. No telling how or if the new Batman fits into any of it.
"The truth is almost all of Peacemaker is canon with the exception of Justice League… which we will kind of deal with in the next season of Peacemaker,”.
Sounds like they are going to address the inconsistency in Season 2.