Passport Other Names

Are you sure it's not referring to middle names?

Yeah it gives a box for first name and surname, and asks if you have ever gone by any other names

That means legally then, as in if you changed your name by deed poll or through marriage then put down your previous names. You don't need to put the one you're only using in college down.
Although on another note, make sure your college doesn't enter you in for qualifications for your assumed name - you need your legal name on your certificates.

Hi guys, I’m applying for my first uk passport. It asks whether I go by any other names; legally I don’t but in college my preferred surname is different to my legal one. Do I need to say that or does it not count as it’s just preference? Many thanks.

That means legally then, as in if you changed your name by deed poll or through marriage then put down your previous names. You don't need to put the one you're only using in college down.

There are lots of scenarios where people go by more than one name without having changed it by deed poll or marriage -- a some actors and other celebrities use stage names without having gone through any kind of legal process to change their name; and some people use one name professionally and a different one socially (for example, a academic who changes name on marriage might continue using their previous name in professional contexts for continuity, particularly where they have a significant set of publications in that name).