I never thought that Chromebooks were suitable for running native applications because of that tiny hard drive space. Cheap but good certified refurbished laptops (particularly ThinkPads) are much better in general in my opinion. But since you own a Chromebook and want to use it for Quelea we’ll have to make do I suppose.
I’m surprised that 16 GB is not enough even to run two operating systems though, maybe Chrome has a very big cache or you have a lot of GNU/Linux apps installed on Chrome OS?