I do not have a problem with Vortex doing things automagically for the average user. It's great and makes things easier and makes mods more accessable to more people, to a point. But rules and groups are not a way to fine tune anything.
Maybe I've just been really lucky, or maybe it's due to me still modding and playing original Skyrim, but after putting less than 10 plugins into another gorup 6+ months ago I've not had to do anything else with sorting plugins. So at least in my experience groups is enough to fine-tune my plugin load order.
As for doing things manually, let's say you've got plugin A, B and C and you drag-and-drop C before B. This can mean:
1: Absolutely nothing, in case A, B and C is independent of each others.
2: C is just a short stop on further drag-and-drop before A.
3: C must load before B, but location of A is irrelevant.
4: C must load after A, but location of B is irrelevant.
5: B must load after A, but location of C is irrelevant.
6: Plugins must load in exact order A -> C -> B.
Now if overlooks 1 and 2, where's 4 different possibilities. If you're never ever going to do any more changes to the plugin load order, it doesn't matter if you mean 3, 4, 5 or 6.
If you on the other hand sometime in the future add plugin D and where's a LOOT rule that says "load A after D", it's important to know if you meant 3, 4, 5 or 6. Only if you meant 3 are you guaranteed the new rule won't screw-up your manual plugin load order. For 4, 5 or 6 on the other hand the rule can be enough of breaking your manual sorting.
This means, your choices are:
a: After the first time you manually sort a plugin, you only uses manual sorting, since this will guarantee nothing screws-up your manual plugin load order.
b: Every time you've auto-sorted the plugins, you must verify and possibly repeat all the manual sorting-steps.
c: Based on you're meaning 3, 4, 5 or 6, instead of manual sorting plugins you put one or two plugins into other groups and afterwards you continue using auto-sorting of plugins + custom rules.
All options a, b and c can give your desired plugin load order, but personally I choose option c, since while it can take a few seconds longer for the initial setup, I don't need to repeat the manual step sometime in the future when I likely has forgotten plugin C was moved at all.