To set the context, I'll remind that the map (galaxy) files generated by Galaxy Forge (GF) have both a global/galaxy section for the planet upgrade levels and per-planet sections of the same levels. (In contrast, the in-game Map Designer produces maps that have only a global/galaxy section for the upgrades because it uses the random generator for the planets, rather than detail them.)
Editing the global/galaxy planet upgrade levels from within GF is not entirely obvious. You need to have no planet/star selected (i.e. have click somewhere on the background) for the global/galaxy settings to show up at all, and after you do that the global/galaxy settings related to planet upgrades are misleadingly listed then under "4 - Home Planet" in the GF Toolbox.
Furthermore, whoever wrote Galaxy Forge seems to have assumed that the per-planet upgrade settings, which you can edit from within GF once you select a planet (these are listed under "6 - Advanced" in the Toolbox then) override the global/galaxy upgrades, but this is not how the game engine treats the sections in relation to each other. In the game engine the per-planet upgrade levels are added to global/galaxy ones. For example, if the global section has "quickStartHomePlanetUpgradeLevel:Infrastructure 3" and the home planet section has "quickStartUpgradeLevelForInfrastructure 2", then the actual level computed by the game engine is 5! (You can convince yourself of this by decreasing either the global or the per-planet counter by one; it will have no effect because the resulting level would still be 4, so the planet will still start maxed out.) As another example, [the galaxy/global] quickStartHomePlanetUpgradeLevel:CivilianModules and TacticalModules are both set to 3 by default in GF-generated maps, but the per-planet ones are set 1 (quickStartUpgradeLevelForCivilianModules) and 0 respectively (for quickStartUpgradeLevelForTacticalModules) by default. "Despite" these lower per-planet settings you get them maxed out too in the game.
A less confusing/buggy way to generate the per-planet default sections given how the game engine accumulates the upgrades would be for GF to all set the per-planet upgrades to 0. The obvious workaround for now is to edit the resulting galaxy in a text editor before playing it... Alas you cannot just delete the per-planet chunks from the GF-produced galaxy file; the game engine will give lots of failed assertions if you do that because apparently all those lines are mandatory. You need to zero them out instead.
Finally, this OP initially contained a different bug report, but that was incorrect; I had assumed the upgrade levels failed to save properly in GF, but since nobody replied to it, I've replace the original text with the actual issues found after more digging.