Thank you for the feedback, I passed it on to our lead designer. There are some known bugs with planetary improvements/upgrading and the other bugs mentioned have been added to our list.

[Bugs] Starbase module prerequisites: +mp, +rp out-of-sequence; +ap/+bc cross-benefit upgrade

I expect all starbase modules to get reworked.  I dunno if these are bugs, anachronisms from incomplete editing, or ... design intent.

"C2" means tier 2 in the Colonization tech subtree.  For Terrans, C1-5 = Age of Expansion, C6-8 = Age of War.

• Manuf module upgrade path (these replace each other):
• C2 Xeno Industrialization: Starbase Factory +10% ==>
• C4 Advanced Construction: Zero G Scaling +15% ==>
• C6 Precision Manufacturing: Orbital Replicator +25% ==> (dunno yet ... the C8 tier?)
• Manuf out-of-sequence:
• C5 Practical Fusion: Interstellar Collector +25%, 2 constructor pts has prereq C6 Orbital Replicator

Research has a similar tangled hierarchy, but it's even worse, as it goes up to C8.

• Research module upgrade path:
• C4 Institutional Research: Starbase Laboratory +10% ==>
• C6 Research Centers: Zero G Experimentation +15% ==>
• C8(!!) Integrated Research: Orbital Research Center +25%
• Research out-of-sequence:
• C5 Research Coordination: Orbital Institute +25%, 2 constructor pts has prereq C8(!!) Orbital Research Center

You can research the C5 tech in Age of Expansion, but you won't get the starbase double-module jackpot until much, much later on.  The net effect is a nasty surprise for the new (Beta) player.

In the Governance branch, the new Approval modules are stuck in the Wealth upgrade paths.  So taking a later +wealth% module replaces your +approval% module.  Also, it's a nasty tree with many choices, not a linear path.  Does the unwary Beta tester get trapped down the wrong tree path?

• Stand-alone, not in any upgrade path.  Hence, it stacks with everything else.
• G2 Xeno Commerce: Starbase Market +10 Wealth
• The rest seem to form a tree.
  
• G4 Xeno Entertainment: Recreation Center +10% Approval ==> (upgrades to either)
• {
• G4 Xeno Economics: Orbital Shopping Center +15% Wealth, or
• G5 Xeno Tourism: Orbital Resort +15% Wealth ==> (upgrades to either)
• {
• G6 Population Diversion: Zero G Ballet +25% Approval, or
• G5 Interstellar Banking: Starbase Promenade +25% Wealth
• }
• }

• The last 2 are not upgrades, but coexist with their prerequisites.  These aren't buggy; I include them for completeness.
• G7 Financial Sectors: Franchise Center +25% Wealth, +25% Influence has prereq G6 Zero G Ballet.
• G8 Superior Recreation: Zero G Arena +25% Approval, +25% Tourism has prereq G5 Orbital Resort.

[Edit] Starbase module prerequisite trees seem to be inclusive (you may take all branches to all leaves), not exclusive (you must commit to 1 root-to-leaf path).

• When you upgrade module A to B1, A vanishes from your starbase's installed modules list, and you no longer get its bonus.
• If A is also the prerequisite of another module B2 (and its subtree), you may later install module B2, even though module A is no longer visible.

Just send more (double-)constructors.

That's how they work, as far as I can tell.

It is working. The problem is, that Environmental Research actually provides +1 level to Manufacturing improvements, while Environmental Manufacturing provides +1 level to Research improvements. Also, you have to wait a turn before the bonus gets applied.