I think people are using 'scales' in a broad sense here - to include the relationship between notes and everything that comes with that.
I have been playing a long time, and learnt my scales and modes quite early on... but I am still now working to understand both how you use and substitute chords harmonically within a key, and how a piece of music can move within keys... and then how you can apply modes over the top to give you structured and 'thought out' ideas over the top.
I had a great chat with a jazzer friend of mine about the great jazz solos, and he explained there were some players who just closed their eyes and blew vs. some others who planned and structured their solos in advance... 2 very different approaches with merits / issues. I have always subscribed to the view that 'd rather understand WHY something I did worked/didn't work than just trust to feel... and whilst I have learnt a chunk of theory, I am still fundamentally a feel player.
The other thing I think is a huge advantage of learning your scales & theory is how you can apply the logic of theory within a song... so even if you know nothing about the song, you can usually deduce the key from a bit of ear training (and spot the 7th) and then you have the building blocks of the song... and can follow/provide effective counterpoint to the melody even if you've never heard it before.
Sure you can just do this by ear, but thats a lot harder and riskier imo - and when you play a dep gig with an 'adventuring' guitarist who likes the crowd to decide what you are going to play, a more reliable approach makes sense.