With regard to usage I would say that it's somewhat commonly used, specifically in (news) reports: https://www.google.com/search?q=%22saw+an+increase+on+last+year%22.
With regard to grammar I imagine that it's a slightly abbreviated form of something along the lines of: "This year's harvest saw an increase of 5% on top of last year's harvest". There's last year's harvest and the increase is 'on top of' that of last year, which is probably why the 'on' preposition works. At least, I feel like it is. If you put it in a more conversational sense, you'd get: "I put in 3 potatoes on what I usually do". It's the same type of structure, but you clearly need 'on top of' here. It's not extremely thorough, nor backed up by any grammar book, but it feels to me like the "saw an increase on last year" structure is an abbreviated phrase used solely for that type of reportage.
But I get why you'd be more inclined towards other ways of phrasing it, but I'd avoid 'since', which indeed indicates that the entire period between point A and point B was required to reach a certain increase ("Since last month I've collected three rocks!"), as opposed to comparing two points in time (Compared to what I got last month, I collected three more rocks!").
My personal preference would go for something like "Compared to last year, this year's harvest had an increase of 5%", but that's likely because I don't do much in the way of reporting for longitudinal studies or projects.