[relentlessflame]

Well, first off, I think your phrasing of "most anime/manga" here is a bit leading. Most anime and manga do not deal with topics like this. This kind of issue is mostly concentrated in a specific subgenre (mostly shounen power fantasy and RPG-inspired isekai). The wisest advice would be to just avoid this subgenre entirely, or at least specific works that frequently employ this particular tactic.

Besides that... it's basically just authors wanting to have their cake and eat it too. They want to deal with "dark" topics and have a protagonist that is more edgy/"evil" than the typical straightlaced Lawful Good everyman, and so the easiest way to do that is to have them do things we'd otherwise see as crimes. But, at the same time, they want people to be able to relate to them and so understand their internal rationalization, and not necessarily see them as "unredeemably evil." So it's a conundrum -- how can you have a protagonist that does "evil" but still be seen as "the good guy"? And yes, it usually comes down to rationalization -- either the world setting itself justifies otherwise unacceptable behavior, or the specific circumstances justify it somehow. Sometimes this kind of rationalization is also the otherwise-unseen hand of publishers/editors/ratings boards trying to prevent the work from going too far "over the line" (even if the rationalization is silly). (When Web Novels get officially published as Light Novels, and if they eventually get adapted into Anime, you can sometimes see this at play.)

Some of it is just clumsy writing, too. Writing a compelling evil character is often very hard. The author may want to put the reader in a position where they can see why, given the circumstance, the protagonist may do certain things that would otherwise be evil. But if the surrounding circumstances were too contrived/convenient, it lessens the impact of what could otherwise be an interesting look into a character's psyche.

If you consider a work a power fantasy for the author and the reader, having these kinds of rationalizations (even if silly) is what makes it a "safe fantasy." It reminds you that this world is not real, the circumstances are not real, and so you can imagine yourself doing an evil thing that you'd otherwise never do. Sort of like roleplay (and a lot of isekai works are inspired by RPGs). That isn't to say that all works need to be engaged in this way, but it is a way to engage in them for some.

All in all, for me personally, although I do find these kinds of rationalizations often a bit silly, it isn't necessarily enough to completely ruin a work for me as long as there are other interesting/redeeming qualities. (It depends on what the protagonist does, of course.) But everyone's different, so maybe in your case you just have no tolerance for this trope -- and, in which case, yeah, definitely avoid works that abuse it.