Current numbers on RW militaries view average world-wide active duty participation at 2.5 military members per thousand population (0.25%) and at 9.6 per K (0.96%) when including reserve and paramilitary forces. Among the 15 countries that spend the most on their militaries in total USD equivalence, the rates are slightly lower (2.0, 7.1 per K), which makes sense in that their forces are more likely to be mechanized (armored vehicles, air forces, naval vessels) rather than just infantry. Using this as an example, a typical stellar nation's active-duty military might be equal to 0.2-0.25% of the population and its total military around 0.7-1.0%. If a given planet has a planetary population of 1 billion individuals (a developing colony of human analogues), a 0.2% active-duty segment would be 2 million individuals and a total commitment of 7 million.
According to the Wiki, each Colonist on a planet contributes one Defense Army, with some jobs providing a higher number (although these will be a limited fraction of all jobs on a planet) - I'm figuring on average that a planet has around 1.1-1.2 Defense Armies per Pop. Also per the Wiki, any of the more typical Assault Armies (and their variants) are limited to 1 per Pop (and specifically no more than 1 per Pop of the species used to make the Assault Army) - there are allowances made for armies not based on a species (e.g., clones, xenomorphs), so depending on their inclusion in a military, Assault Armies could be perhaps 1.0-1.5 per Pop. That's around 2.1-2.7 armies per Pop in total.
The number of Pops that can live on any given planet can be all over the place, depending on the size of the planet, the number and types of districts built, the number and types of buildings constructed, tech bonuses, etc., all contributing Housing (needed for each Pop). Each resource or industrial district would provide 2 Housing, other urban districts provide 5-6 Housing, housing buildings provide 3-10 Housing each, and on down the line. A size 25 planet could easily have way over 100 Pops (it's been quite a while since I've actually played the game, so I'm basing this off of the Wiki). Just throwing a number out there for the sake of the discussion, but if a single Pop is viewed as 250M human-analogue population (and a 100 Pop planet would be 25B individuals), then the population in a max armies scenario above (1.0% of population, 2.7 armies per Pop) would be 2.5M total and less than 926K per army - at the lower end, it's 1.75M total and around 830K per.
What single vessel is going to be capable of carrying 830-926K individuals, plus surface transportation, equipment, rapid-built facilities, and supplies, along with large numbers of shuttlecraft for rapid delivery and possible fighter escorts? All of this needs to be built on a ship that is also <Wiki> "automatically upgraded with the latest defense components" (I read that as Shields and Armor). A Colony Ship effectively carries 1 Pop to the new planet, although I head-canon Colony "Ships" to instead be fleets or convoys of less-ludicrously-large ships, perhaps 25x 10M-person ships. An individual Colony Ship is going to have fewer shuttles (if any, since the ship is designed to land - well, once) and more of its facilities, transportation, and equipment requirements would be met with 3D-printing and similar production on-site, with more dense supplies and materials taking up the remaining volume/mass of the cargo holds. As indicated above, a combat transport would have lots of shuttles, staging areas, pre-built equipment, etc., along with the defensive systems - I don't know if the transport's needs versus its smaller group of passengers would require it to be as large as a single Colony Ship, but it would be in a similar size group. If this transport would be too unwieldy for any type of combat, a similar concept to my head-canon Colony Fleet above could be used to make smaller ships in an "army fleet" (although a distinct fleet rather than a repeating line of individual ships).
Now, whether you feel that the vanilla 1-vessel Colony Ship is unrealistic or not, it's established in the game that the technology exists within the game to build and move units representing MASSIVE numbers of individuals and all of their associated effects. Specific numbers can be adjusted up or down per army, but I think I've laid out a fairly clear set of parameters that put Assault Armies and their transports well within the paradigm above for even Colony fleet ships.