Daredevil and Punisher were way to different from the tone and style of the movies, there was no way they were going to release movie versions as part of the MCU without changing them to match the style of the rest of movie.
Not necessarily; historically, comics have had characters of different tones / execution meet and it worked while still operating in continuity (e.g. The Brave and the Bold, Marvel Team-Up, etc.), usually because the story recognizes and plays up the differences before a conflict could be resolved, yet no character is compromised. Its the reason I've felt the Netflix Punisher could appear in a Spider-Man movie (it does not have to mirror how he was introduced in The Amazing Spider-Man #129) initially as an adversary, or perhaps something long term. The Sony/MCU Spider-Man has to grow up, and his world--and risks--should reflect that as he fights crime on the streets (instead of anything to do with aliens / sci-fi elements again and again).