Hi again Zarnoo!
You're absolutely right. I've actually been worried about this since the 0.18 update. I started storing a lot more information in the global table to increase performance, hoping that the 0.18 factorio improvements would counteract the increased save/load times. My test environment seemed to have acceptable save/load times, but I've been waiting to see how it handles real-world games.
I just uploaded 0.18.5 that adds Performance Mode as a mod setting (default disabled). When disabled, this setting prevents a lot of information being stored in the global table at the cost of some UPS. If having it disabled doesn't cause noticeable lag for you, then it should reduce the mod's save/load impact by ~75%. Note that you'll only see this improvement after updating and then saving with mod version 0.18.5.
As for the number of items loaded, the mod actually uses hidden inserters to load items, since doing this via script is much slower when entity numbers get to midgame levels and later. Since inserters load a pre-determined amount defined in each entity's data stage (factorio loading screen), I can't really change this number at runtime. I would have to change this value for each entity's data.raw definition, and this would cause problems when trying to use these entities in normal gameplay. This has actually been a point of frustration for me for a while now.
That said, I increased the speed of the mod's inserters to see if this might help alleviate your supply issue. If it doesn't, let me know and I'll see if I can come up with another solution.