I completely agree. "Main" scientist sounds very awkward for anything regarding people. For items and objects it works, but not people or positions, it seems.
I thought "head" was reasonable, but it's not accepted. I think we are more likely to talk about a "head scientist" than a "main scientist", even if it's not an official title. We'd still be referring to the person mainly responsible. "Lead scientist" is another term that might be used.
In English, "chief scientist" (with lead, head, senior as alternatives for chief) sounds more natural than "main scientist."
It can refer not only to a 'scientist' but also to a 'scholar'. The Russian word нау́ка is usually broader than the English science. Нау́ка covers not only natural sciences but also humanities. Therefore, since учёный is someone who занима́ется нау́кой, this word can be translated either as 'scientist' or as 'scholar', depending on the context.
This is unlikely to be a title, because the word учёный is not usually used as an official title. Instead, formal titles are likely to be "гла́вный нау́чный сотру́дник" or something like that.
Head, Senior Scientist should be correct as well....in fact they should be primary variations.......