@tseitsei89, You can still do everything you want without any changes to the mod and still use that 2.5m kontainer. But, what you will need to do is have a design that lets you actively push supplies into planetary logistics. What you say is true, it will take a long time to push supplies into PL if you rely on just the passive push.
Not sure how your base is designed, but here's a simple base setup that would do what you want with two base structures:
1) one of the planetary logistic modules (Duna Logistics or Tundra Pioneer) with a quartermaster and a small kontainer for supplies (ISM is great for this)
2) an agro-producing module with a large (as large as you want) kontainer attached for holding supplies
These structures, of course, need to have power and be 150 m from each other. Now, when you have enough supplies in the agro structure, you simply use local logistics to push the extra supplies into the small container in the logistics structure. These will quickly overflow to planetary logistics which means any remote mining rig will be able to start pulling supplies.
If you want to speed up the process of getting supplies into PL, then just drop a ship near the base with supplies and use local logistics to push them into the logistics structure.