I've been described as 'not conventionally attractive' at least twice in my life (probably many more times!).
Once by a partner and once by my MIL (before she was my MIL).
Neither relationship were /are negative and I don't believe either we're trying to be mean, just factual.
FWIW I do consider myself ugly, however I have some features that in isolation can be seen as attractive. The combination on my face however does not work pleasingly and I do not look at photographs of myself.
Has anybody ever said this, or thought it, about somebody in any way other than a 'polite' way to just mean ugly?