Binged the last season of Sengoku Youko, it's meh. I don't know if it's the anime adaption, but the pacing of the second part is just horrendous and having multiple long flashbacks in a climatic fight is a writing sin.
The anime has several issues, it's not a Biscuit Hammer tier adaptation but I'd hardly call it a good one. Skipping or distorting content and changing the pacing are some of its obvious sins. At least some of the best episodes (like the shogun fight) stand out.
it just flip/flops between fighting is good/fighting is bad
I don't think it does, at least not in the manga.
One of the author's main strengths is being very rational and not talking out of his ass. If he's going to preach something then he'll acknowledge the caveats and opposing viewpoints.
Generally speaking, the author advocates for exercise and healthy competition which is why some of its most competent characters (in life and spiritually) are big fightfags (like Tiger). The pursuit of power is never treated like it's a bad thing and more like a responsibility (which is why dragon guy isn't necessarily blamed for putting his son through the experiments, he had some valid reasons for that). And finally, regarding killing/violence:
As an aside, I really fucking hate anime doing "killing is wrong" moralizing when the heroes and their friends are invulnerable to damage from mooks, and have a literal friendship no jutsu. If you are playing pacifist then you should at least have it be dangerous to yourself, otherwise it's the morally equivalent of "don't kill grade schoolers if they get out of line".
It's never implied killing is a mortal sin or anything by the author. That's why Shinsuke gets some kills in, even in revenge without getting blamed for it (which is something we don't see enough in fiction imo).
When Senya wants to go for the no killing route, it's not because he has no right killing anybody, the monks even say so: voidfags took many hostages so it's going to be a real challenge to try and spare them all. The reason Senya goes for this is because of the spiritual roots of his character arc, he's not just a human being, he's growing up to become something more (hence the Senju Kannon and praying headbuddies). And it's a challenge, he did have a pretty tough fight against that army (at least in the manga).
But yeah, the author's point is more about avoiding killing when it's possible, not about anything being absolute. Similarly, revenge isn't being shunned by the characters, I'm pretty sure Shinsuke didn't do anything wrong.
I'd advise taking a look at Spirit Circle (6 volumes) if you're interested in the author's works, it has a few interesting moral dilemmas. The sleeping tower one is the most interesting imo.