It was intuitive in the sense you could always build a greenhouse, but it's not intuitive mechanically because it's not built anything like a real greenhouse (you could of course argue that everything in VS is built in such a fashion but I digress..), nor does it operate like one. The properties of light, glass and crops in Vintage Story are a little too abstract for this to be anything intuitive.
As for the greenhouse/cellar size limit, that is debatable because I don't see why it has to have a size limit any more than the world has to have limits. If the day comes where we can have sprinklers or drifters watering our plants, then I'd definitely want to see it revised either way. I'd also like to have players forced to clean/repair the glass every month for maintenance
If I got into greenhouse size on the technical side I'd be here all night, but I don't think calculating room size is a technical hurdle in the scheme of things, it is however, another task on the plate. I do think it is nasty when you make something one block too big and all of a sudden things some things just don't work. As you said, not intuitive in the slightest for greenhouses and I would argue cellars to some degree as well. I imagine these hard size limitations are semi-temporary and will possibly be revised someday. They're not huge issues but they greatly affect food and farming mechanics.
Which is why I thought a mechanic where you could be allowed to grow the next tier of warmer crops (or frost immunity) may be a more beneficial and clear-to-the-player game mechanic than going with a fixed value which is every bit as unrealistic in the first place. It would then always have a clear impact on gameplay, regardless of your biome and everyone can make use of it and identify with (similar to getting access to a new metal, a new level of civilization literally). If you're arguing that adding +5C is more realistic than Stardew Valley, well, it is every bit as unrealistic anyway; My point is not about realism so much as it is that greenhouses sound a little unintuitive and questionable in execution as Gazz found out, and I'd like to see a bit more to them than fixed numbers and sizes.