The mods actually include or remove lines of code while the console just changes values.
The big issue with mods adding or removing (particularly adding) lines of code is when you save the game, it saves at the location within the script. If you open an unmodded game and try to resume where a modded save last pointed to, that location may not exist or is some other way compromised. Then the game crashes.
If you just use the console, nothing is particularly compromised unless you've modded values in such a way that mutually exclusive conditions are both met, but that won't crash the game, it'll just be potentially unpredictable.
If the mods just added an intuitive interface for less technically minded people to change values, that'd be fine (there's still the risk of the game crashing when updates occur and you haven' reapplied the mod), but what I dislike about the mods are when the modders take liberties and literally change the game. That's why I don't use mods (unless I'm doing it myself, in which case I know exactly what's happening behind the scenes).
It's fun to bash a character. I like all the characters in the game (except the Madame

), but that won't stop me from putting the boot into someone like Jill from time to time.
They are not real, so there's no harm with being mean about them.
When other people get upset about that, the people getting upset need to take a step back and realise most of it is in jest, and even if it's not in jest, none of it matters in the slightest compared to literally everything else in life.
The only thing I don't like to read, are people writing vitriol towards DPC. The man works hard and has created an unarguably fun game. It's not for everyone, so disliking the game is fine, but there's never any need to start bashing a real life person who has earnestly created something (that's not to say you can't comment or criticise his work).