Well, if the Library section of DOA6 is of any indication, Genra being evil from the start per DOAD may have been re-retconned (since the Library indicated that he was brainwashed like in DOA3 originally).
I'm hesitant to say the first DOAX is non-canon, regardless of whether Itagaki says it or not, since it did formally introduce Lisa and Niki, who did appear in later games, the former as an official fighter, and considering they actually teased DOAX2 in two of DOA4's endings (specifically, Zack and Kasumi's respective endings), it's extremely unlikely that's non-canon as well. If they were truly non-canon, Lisa and Niki would have gotten the same treatment that Chris Jenner, Black Chamber, Wiseman, and the like got in Metal Gear Solid overall, not even be alluded to at all, let alone have any appearances. Or for that matter, how all the Dragon Ball movies are non-canon and aren't alluded to at all save for Dead Zone (due to Garlic Jr. having a saga dedicated to him later on that has direct references to that movie, not to mention Super directly referencing Maron, a figure from that saga, later on in at least the anime version), and possibly Tree of Might (due to Icarus frequently appearing in the anime after debuting in that movie) and Cooler's Revenge (due to Cooler's cameo in GT, though that's ambiguous, especially when GT itself has very shaky canon even without Super.).
DOAX3's in the gray area, especially when DOAXVV has Honoka specifically mentioning winning a vacation ticket in a raffle again, referring to how she earlier arrived at Zack Island in DOAX3. Besides, unlike prior DOAX games where the girls clearly interact with each other outside of volleyball or minigames either regarding their opening scenes when a partner is selected or otherwise the be friendly gravures, DOAX3 barely even has the girls interacting with each other at all barring certain matches, so it's pretty much left ambiguous as to whether any of them actually interacted at all during their vacation. Heck, some of the cutscenes, namely the beginning and ending of each girl's vacation, also imply they may have literally been alone during the vacation barring maybe the Owner.
Well, to be fair, just going by the actual cutscenes, it's left ambiguous as to whether the girls ever actually interact with each other at all in that game. Let's not forget, unlike in DOAX1 or DOAX2, which not only had Be Friendly gravures where the girls explicitly interact with each other, but choosing a partner actually has a cutscene where they talk to each other (case in point, the scene where Lisa teases Helena about Zack having romances in the deepest parts of space in reference to Helena's invite in DOAX2 involving bringing peace to the galaxy via DOATEC if you either choose Helena or Lisa as your partner and you're playing as vice versa.), DOAX3 actually lacks any character interactions between the girls in gravures, heck, even any cutscenes where the girls interact if you choose them as a partner. In fact, the closest thing to their having any interactions is during gameplay regarding various minigames. And that's not even getting into how the opening and endings for each of the girls heavily implied that, barring the Owner obviously, they're completely alone during that vacation (for example, Marie Rose is hesitant to leave Helena after she dismissed her from her duties, and Ayane in her ending makes very clear she could not find ANY trace of Kasumi on the island despite the intel.).
Not to say I even approve of DOAX3 as being canon, especially when DOAX3 has many problems of its own (for starters, aside from gutting a lot of stuff from past Xtreme games, it also made some characters regress in development, like for example Ayane. I thought she buried the hatchet with Kasumi, so why the heck would she still be trying to hunt Kasumi down in that game, even if it WAS just an excuse to take a vacation?). But nevertheless, you'd need more than that to claim it's non-canon. Now, if DOAX3 had actual character interactions BESIDES gameplay-related like be friendly gravures and/or any cutscenes that play when choosing a partner, then you might be on to something.