Glad you found the resolution flowerpunk!
The megawar in my megagame has begun and its just ginormous! The game works perfectly well for me, fleets and ships move (or not) where and when I tell them and I am not having any trouble controlling/refitting/ordering literally many hundreds of ships. Believe you me, at the scale I am playing and a few hundred years into the game I would very much have noticed and prolly gotten hot under the collar if things were discombobulating my plans.
Get to 1000+ state ships and declared war - whether year 1 or year 100 in game, unless you use a VERY specific set of settings and manual control - with many factors that can engage autonomous behavior - then ships and fleets will act autononmously, sometimes in irksome manner.
Is it possible to have full 100% manual control? Of course. But it is not imo the norm, or as normal sounding as your post suggests. For example, not even a partial list but of the many popular and very useful mechanics players can and should use, the second you:
1. Enable and use attack fleet posture at all, even for fleets set on 'manual', fleets can and will move autonomously - far outside the specified attack range.
2. Enable and use defense fleet postures - fleets can and will move outside the specific range you thought you had setup
3. Use any of handful of various factors that can trigger a refit of a single ship or class, can and will move entire fleets off position at wrong / worst / inconvenient moments in autonomous fashion
The only way you can ensure 100% compliance that no state ship - e.g. your 'real' military ships and fleets vs who cares private sector - will move autonomously is to turn off every aspect of ship, fleet, and construction automation to disable advisor prompts, refits, fleet attack and defense postures, fleet percentile logic for auto reformation / refueling due to scattering, etc.
What makes a game 'not scaleable' in terms of empire management or micromanagement are purely relative and playstyle specific - so i will never impose my definitions on yours. If you are happy with how you are able to manage your game, awesome.
But what is factual, and not opinion, is that autonomous behavior of state ships is so deeply woven into the game, it is possible to have 100% full manual control but requires disabling a laundry list of helpful game mechnics, not the least of which are the very powerful and useful fleet postures for attack and defend.
I wont contradict what you are saying per se but I'd suggest either looking more closely at what ships and fleets are sometimes doing, or you do indeed have full manual control but imo your post is attempting to make that sound more the 'norm' than it really is.
You dont have to try much at all to use and integrate state/private sector automation, one of the core differtiators and brilliant aspects setting this vs other traditional 4x games apart. But you really, really have to try in order to play as full manual as you imply.