I'd like to point out that by the time you begin Mission 13, the Kusari Navy has already been defeated and mostly destroyed, Rheinland forces are in New Tokyo, and Liberty has invaded Shikoku. It is unclear how serious engagements between Rheinland and Bretonia are, but the statements I just made are not conjecture, they are part of vanilla. I've played it through eleven times, if you don't believe me play Mission 10 again (the first part, mostly). The further successes of the Rheinland Military can be found if you talk to the people on the Osiris, as well as if you listen closely to some pieces of dialogue in the last three missions.
A civil war in Liberty was already happening, from Mission 4 until Mission 11- it was, however, small enough that it was able to be glossed over. After Mission 11, it appears that the remaining guerrilla fighters had been recruited by the Order: at any rate, they are no longer a concern to Liberty. Further dissent would need a miracle to snowball into something meaningful without being brutally cut down.
Let's also remember that in vanilla, a lot of factions did not have the impressive navies they do today- the Blood Dragons were a guerrilla power, and burned up most of their resources in the Battle of Tekagi's Arch (Mission 9). If a lot of these factions had capships during the SP campaign they certainly would have used them.