The way I solve it is removing all the shield generators before exiting and then putting them all back after I come back.
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I found enemies tend not to understand how to flank and how to use weapon rotation to their advantage. they also do not know how to target weaker or more critical points. they really do not know hot to dodge either nor do they keep their flanks or critical systems away from fire. Last bit is their construction is a bit hodgepodge where shields are in the middle weapons and engines are near the edges and the core is dangling underneath or exposed on the top. I know making a dynamic engine take into where hard points should be and where critical systems should go is a bit tricky. They also do not know how to use guided missiles so you can trick them by blasting up or falling which will cause the AI to retarget to lead the player for a new shot which causes the missiles to veer off away from the player.
and I was able to beat it including the last boss! second life and a quarter island left but it worked barely. Use all your blocks and spykes land on the top of the final boss (keep crashing into it you should have tons of layers) and fire everything you got straight down. If you have the right loadout you should be able to drill through the top and get to its core before it does. The other way is have a very very fast ship and keep its targeting system going in circles. You will need some of the scatter shots for the shields and a decent main weapon.
to fight everything else out there just keep out of their range and take pot shots at them. also you can go from the very bottom to the very top which will usually make them overshoot and take out of bounds damage (you can help this out by firing ontop or below them)
I found a bug ... accessories added to armor or shield generators do not survive a save. The addons do not get written to the save file at all and subsequently are lost forever. The addons do seem to stay there until you leave the game or go to the main screen.
EDIT: the mod parts are saved to the save file when exiting but they are not loaded back when reloading the game...