Not sure I really follow your downside. Maybe I haven't got my head around all the terminology used.
A (singular) Question has (plural) Options.
Each Option has (plural) Pros/Cons that can be unique to a particular Option.
Each Option also has (plural) Specifications that are common across (plural) Options.
Each Specification can have (single/plural) Choices? (the four column types mentioned)
The filter idea is to include/exclude Options based on Specification Choices. I was thinking about this for the Compare all specs popup pane. So I'm not really getting why order would be a problem here. Indeed in that popup view it would be nice to see ordering be user selectable. (i.e. order by ascending price, then by ascending file size, for a contrived example)
Perhaps you are thinking of filters applied to the Questions themselves, and that's why I'm getting confused?
The separate question for each context sounds horribly noisy on its own. Wouldn't you end up with hundreds of minor variations of each Question?
Again I had the Spec info popup in mind when thinking of this, and having the rows categorized, and being able to collapse them out of view. Assuming I could click on Editor and collapse that section, then sure that's the general idea, but again, it's more about the specs where you could potentially have hundreds of rows (i.e. a comparison of art programs) although I can also see the value in the categorization of the Pros/Cons in your link too.
Think of a spec (feature), but it was only added in a recent version. i.e. Terminator recently got some fixes to run under Wayland. So the spec "Runs under Wayland" would be a green tick mark for Terminator, but a small annotation marker would present a popup if hovering over that cell. In there the text would say "2.0+", so people understand that 1.0 will not work on Wayland. Other options (i.e. Guake which uses gtk2) won't run under Wayland, so would have the red cross. Of course they could add their own annotation that it will be in the next release.
It could also be used for explaining a feature, by hovering over the column header.
Slightly off topic question: Terminator suddenly jumped to the top of the "best Terminal" question mainly because Pantheon dropped two places despite having more recommends than any other option. Was that a new adjustment due to brigading by the elementaryOS people that I read about on some other posts? If it was just below Terminator I might have put it down to my Karma somehow boosting Terminator.