This change is one I've tried to adapt to but simply just can't get a handle on it.
My designs are often symmetrical (Evenly numbered entities if possible) and only make use of the least needed number and tier of modules to achieve this. That means I'll have different quantities and types of modules per recipe and the priority system doesn't seem to accommodate that.
The old system where I could click on a module was agonizingly slow on larger prints at times, but provided that precision for every recipe. This is especially important with recipes that can use lower tier modules to save on resources while still requiring the same number of entities. (Ex. Where using a Mk1 speed module needs the same number of entities as the Mk2 module, but you need to try both to be sure of this.)
I'm sorry, but It was more intuitive how it used to be. I can't think of any reason I'd want to use the same subset of modules for every recipe when the number of slots can also differ and throw off the goal I'm attempting to achieve. I'd be highly in favor of reverting the change or providing a mod setting to restore that functionality, as I've honestly stopped using Helmod since this change.
Also of note, having too many configurations can cause the button to add more to be hidden behind the modules. The testing methodology really fell apart when I tried to create more than six module sets and couldn't click the plus sign behind the module buttons. This I imagine is an even greater nightmare for mods that utilize many different types and tiers of modules, where a dozen configuration types is normal.
I'm trying not to be overly critical, as your mod has been instrumental in some of my greatest designs with absolute precision using the least amount of resources possible; It's just this one change in particular that has turned it from my most utilized mod into something I seldom open anymore. Unless there's something I've missed, I'd really like to see a new mod setting to choose either method as both systems do have their merits.