Basically it anything that is built in space does not interact with the mod. I can set the module configuration but it does not apply when selecting buildings with the tool.

Did you select the grounded versions in the gui? For a lot of SE buildings 2 versions show up in the gui, one version with "(Grounded)" added to the name and one without. The version without works for me.

I'll make an update tomorrow that filters out the grounded versions.

It does not work for me even if I specifically selected the regular non-grounded version. Not sure if maybe another mod intercepts anything so modlist is below.

aai-industry_0.5.3.zip                                                    
aai-signal-transmission_0.4.1.zip                                         
alien-biomes-hr-terrain_0.6.1.zip                                         
alien-biomes_0.6.3.zip                                                    
Bottleneck_0.11.7.zip                                                     
combat-mechanics-overhaul_0.6.13.zip                                      
Companion_Drones_1.0.16.zip                                               
DeadlockResearchNotifications_1.0.2.zip                                   
even-distribution_1.0.6.zip                                               
factoryplanner_1.1.15.zip                                                 
flib_0.6.1.zip                                                            
GhostScanner_1.6.0.zip                                                    
informatron_0.2.1.zip                                                     
jetpack_0.2.5.zip                                                         
Krastorio2_1.0.21.zip                                                     
LogisticTrainNetwork_1.15.0.zip
LtnManager_0.3.10.zip
ModuleInserter_5.2.2.zip                                                  
Moon_Logic_0.0.49.zip                                                     
pump_1.0.1.zip                                                            
Repair_Turret_1.0.0.zip                                                   
resourceMarker_0.6.24.zip                                                 
robot_attrition_0.5.7.zip                                                 
solar-calc_0.1.31.zip                                                     
space-exploration-graphics_0.5.4.zip                                      
space-exploration-hr-graphics_0.5.1.zip                                   
space-exploration-postprocess_0.5.8.zip                                   
space-exploration_0.5.30.zip                                              
Squeak Through_1.8.1.zip                                                  
stdlib_1.4.6.zip                                                          
StoneWaterWell_1.20.1.zip                                                 
underground-pipe-pack_1.1.0.zip                                          
walls-block-spitters_0.6.2.zip                                            
what-is-it-really-used-for_1.6.0.zip                                      

I found the issue. It is not the mod, it was a user error. Still you might want to make a change for that: Closing the config window with 'E' does not change the configuration but it still saves it. It only truly goes through when hitting the green check mark.

I guess I already got too used to things working like that for Logistic Requests and stuff.

It's fixed in the latest version.
Pressing E when the window is open and not pinned will apply the changes. I guess at some point i'm going to get rid of the green button and simply apply the changes immediately, just like vanilla with the upgrade/deconstruction planner.