I should note that I'm very much talking about the designing of combat ships. Obviously you're not throwing on Heavy Armor on a Revenant, and as you say you're similarly never s-modding a non-ADF/Militarized Subsystems logistic hullmod onto a combat ship, but that's a constant between the current version and the suggested alternative, so it isn't worth mentioning.
I'll point out the s-mod mechanic changes the building of logistic ships a lot more than combat ships, because of the ability to ignore the 2 logistic hull mod (the "Dock" ones) limit, which many people seem to discount. If you have more than 2 logistic hull mods you want a ship, you no longer pick the greatest OP ones - you pick logistic hull mod limits ones that will see the most use and don't want to pull off. Logistic hull mods are all equally valuable against that limit - i.e. worth one unit. Some of the more expensive ones also tend to come with trade off (i.e. higher maintenance costs), so logistic + disadvantages tends to lead to more diverse choices of s-mods there. Also, many logistic ships are not OP limited, although a few are.
If there were more limits like that (designed to prevent stacking) for combat hull mods, you'd probably see more diversity (do I want more OP or do I want more stacking of something else where all these hull mods are equally valuable). As suggested in this thread, one could imagine this also occurring if hull mods increased in value when used with s-mods such that they became "worth it" compared to the higher OP hull mods. In the stacking case, they become more worth it because of potential synergies.
I still find the change to be a more interesting exercise but maybe that's because I don't usually have a final build already in mind when I'm designing from the ground up?
Could be. Your building style is certainly effective, but is also probably not universal. I find s-mods have changed how I approach ship building in some cases, as I now do consider things like Expanded Missile Racks and ECCM more. Certainly for my ship builds which had very few hull mods in 0.9.1a, I now have the possibility to consider builds in other directions. But an extra 30% OP would probably accomplish the same things.
In any case, I do also see cutting down on the amount of OP saved per s-mod to be a positive, but I recognize that's a still less popular opinion. That said, I don't think it's true that the less common hullmods would be seen less with the suggested alteration. Lots of times they're less common because they're generally worse than vents and caps, so the only reason you're including them at all is because they're free. I don't know though; I'd have to actually design the loadouts to confirm it.
I don't think it's necessarily wrong to cut the OP per s-mod, but the question isn't really about diversity in that case - but overall power that can be achieved. If player ships are becoming too powerful, then it makes sense to cut the OP saved per s-mod. However, that requires a whole different set of data, across a whole set of player skill levels. I don't think Alex is considering changes to s-mod safety overrides because it is the only hull mod being used, but because s-mod SO ships like the Aurora are just walking up to capitals like a Conquest or Odyssey and blowing them away without any risk. Although that could just be my impression.
If the added benefit is almost entirely through the former, why bother with this dance and not just have story points increase your max OP as Megas says? It's about as (un)interesting as the current style for end builds, apparently.
It feels a bit more lore friendly with building in hull mods compared to simply raising the OP ceiling (like Luddic Path ships), and the icons on tool tips are kinda symmetric (red for free extra bad mods, green for free extra good mods) which I like aesthetically. However, I do agree the experience for building combat ships would essentially be the same. If that change were implemented, I wouldn't complain for combat ships.
However, I would complain for logistic ships. The experience for building logistic ships is different with s-mods because of the nature of the 2 "dock" hull mod limit. One might argue that building logistic ships is boring as you're just optimizing for a few campaign stats, and that is probably true. I still think it makes that chore a little more interesting. Simply adding 1 to the "dock" hull mod per s-mod spent also isn't quite the same thing, as it'd be much more flexible in principle (in practice in vanilla, 5 dock hull mods probably covers everything you'd want on a particular specialized logistic ship). Without some benefit along those lines I wouldn't even bother spending story points on logistic ships.