Thanks for taking your time to answer!
To reply:
1) Every time you upgrade an instruction, it costs more points to fit into template, can you upgrade template itself? Because going from 40 op for a template I to 75 and more is so prohibitively costly, it hardly makes sense to use. It often requires to rip out hullmods that make or break the build.
2) I am not sure, why would it have to be weaker than vanilla hullmods and being stronger makes it OP? Vanilla hullmods are free to use (well not totally free, you need to learn how to use them first for like 6k creds on average, but once you get the modspec, you can place them on any ship for fraction of ordnance points a liminal template would cost). While liminal template requires hundreds of thousands of credits poured in and uses massive amount of ordnance points. In my opinion, it makes them basically useless until you max upgrade them, so there s next to no progression. Why not have a single level of instructions then, but more costly to research, to skip the phase of 'this is not helping, because its weaker than normal hullmods'?
3) Yes, i agree that boosting all the weapons at once is something base game doesn't have. But how useful it is, to have 10% boost to all weapons, when it requires you to let go of certain weapon types? Or removing vital hullmods (like expanded missiles\mags or hardened shields and etc)? Getting 10% more out of your reaper torpedoes is great, but if it comes at a cost of gimping your ammo supply or fire rate of primary weapons, thats not worth it.
4) Lets say we have a ship, thats super concentrated on energy damage, typical high tech brawler with sturdy shields and energy mounts and couple finisher missile mounts. You can give it a template with instructions that increases all damage, while also negatives, that gimp ballistic rate and missile fire rates to give it even more energy damage. All that still falls short when compared to just adding expanded mags hullmod, that boost the burst outputs of most energy weapons that are reliant on ammo. You can have both expanded mags and the damage template of course, so you get more ammo with more damage. But to sustain heavy OP cost of the template itself, you d have to give up op heavy hullmods like hardened shields or you d have to barcode them in, to afford the template. You can get creative with it, but i still dont see how that 10% boost of damage is worth the finagling you ll have to do. You can also extend the range of all weapons! Its cool, but you also have integrated targeting unit, thats much cheaper and give more weapon range than a template. Once again, we can, like you said, stack ITU and a template to get even more range, but that increase would come at a cost of ripping something out, hitting either dps outputs of survivability.
5) Thats true, but once again, those costs make its use cases extremely limited. Like regeneration - to maximize its usefullness, you d probably use it on something like invictus, that gets hit a lot and has a crapton of armor. That would be quite benefitting from regenerating its armor. You can do some crazy armor stacking with smodding vanilla hullmods and then adding regen instruction on top. But the costs of it still ruin it quite a bit and it will hardly be anywhere near as useful on something with less armor.
Its just my 5 cents after fiddling with the mod for a while, so dont take it as me not liking it, rather, i wouldn't even bother writing all this up if i didn't xD I probably will fiddle with the cost balancing a bit, but i am not sure where is the setting that governs how much the template hullmods cost? For now, i guess, i ll just keep upgrading everything, maybe i ll come up with a build that benefits from templates properly.