Did MoO have a ship designer? I assume so. Whereas Civ and MoM did not have unit designers and rarely do their successors.
MOO had one indeed, but the tactical combat was streamlined, and all ships of a given design were stacked together. You had 5 or 6 design slots iirc.
Most modern MoO clones are inspired by MoO2, whose ship designer they copy almost verbatim (although sometimes adding a bit more complexity to it with more control over slot placement etc). The combat of most space 4X games is directly inspired by MoO2's combat. Even the ones with real time combat feel similar to MoO2 because mechanically they're so similar: Space Empires V, Star Drive 2, Astra Exodus. Even space 4X games that don't have manual combat tend to have ship customization, like the Galactic Civilizations series.
Unit customization is rare outside of space 4X, because it wasn't a major part of either Master of Magic or Civilization. There are a few curious exceptions though, which are usually a result of cross-inspiration - Elemental, Fallen Enchantress, Sorcerer King were made by Stardock Entertainment, the company behind Galactic Civilizations. They feature Master of Magic style gameplay but with Master of Orion style unit customization. Since the company behind these games made Master of Orion clones before, it makes sense that they'd transfer some of those features to their non-space 4X games.
But there's also Sid Meier's Alpha Centauri as a notable planetary 4X game with unit customization. Despite its cult classic status, it hasn't been cloned very often, even though the unit customization feature is something a lot of people liked about it. This could easily be implemented in Civilization style games. History with all its weapon and armor innovations lends itself perfectly to the concept. Start with simple clubmen, research spears and shields, upgrade the equipment of your units. Kinda like how Fallen Enchantress does it, but history instead of fantasy. Yet nobody does it, because it's not part of the Civilization DNA.
There is at least one Alpha Centauri clone out there - not just a planetary sci-fi 4X, but an explicit Alpha Centauri clone - that has unit customization. Pandora: First Contact.
And it has that feature precisely because Alpha Centauri had it.
All these examples show that the average 4X development process is extremely cargo culty. "If the game that directly inspired our game had this feature, we will implement it too!"
I don't know whether it counts as 4X, but Imperialism had some tactical combat.
Not really a 4X, more of a grand strategy game.
I liked the way it was abstracted in Call to Power with support and flanking slots.
Yeah Call to Power uses a superior style of auto-resolve battles than Civ's single unit vs unit combat, but it's still an auto-resolve rather than tactical combat with direct player input.
Master of Orion clones and Master of Magic clones usually have tactical combat with player input, either turn based or real time.
Civilization clones usually have some sort of auto resolve combat, or large scale 1-unit-per-tile tactical combat on the world map (rather than a separate tactical map) - but that style of combat only popped up after Civ 5 came out, again proving that most 4X games just clone what the big names in the genre are doing.
One could easily design a historical 4X with Master of Magic style combat, but it's rarely done because MoM clones and Civ clones exist in their own bubbles with little cross-contamination between the two.
Field of Glory: Empires kind of lets you resolve battles in FOG2, so it could count as a historical 4X with combat.
Field of Glory: Empires is not a 4X in any way, shape, or form. It's a grand strategy game that has more in common with Paradox titles or Total War than it does with the 4X genre.
Check my previous post on features that should be in a 4X game and notice how many of those are missing in Field of Glory: Empires. No terra incognita exploration, no free city founding on an open tile map (it has pre-determined provinces), not a big focus on resource exploitation.
I suspect one reason for the lack of tactical battles is that most historical 4X kind of follow the civ Formula of covering a huge timeframe in which warfare changes significantly.
There are historical 4X with more narrow timeframes that also don't feature tactical battles, because it's not part of the Civ formula.
You could easily cover the stone age to the American Civil War with tactical battles, but it's not being done. Meanwhile, as you correctly observed, the Civ5 style of 1upt grand strategic combat doesn't really fit the "stone age to future" model either, but it has become a common way of doing combat in historical 4X games. Not because it's a great way of doing combat, but because it has been done by Civilization 5, and games that clone Civ5 also clone its combat system without putting any thought behind the hows and whys.
Aggressors: Ancient Rome and Imperiums: Greek Wars use old-style Civ combat, where you send individual units against each other and the fight is autoresolved. It's the Civ4 style of combat.
Meanwhile Old World uses Civ5 style combat.
In most cases, it's not even a question of "What style of combat would serve our game best?"
I don't think devs really ask questions like "How would tactical combat impact the strategic game, considering that a good player could wipe out an enemy stack completely and enter a victory spiral?"
They just accept the conventions of their particular subgenre and roll with it.
Civ-like = auto-combat (old Civ style) or 1upt grand tactical combat (new Civ style)
MoO-like = tactical space battles with ship customization, either turn based or real time; planetary ground combat is auto-resolved though
MoM-like = tactical combat, usually turn based