I would like to provide some details on this:
Apparently this can be reproduced in factorio outside of the miniloader mod by setting up a fully saturated high-speed belt that ends on a single low speed belt with a high-capacity stack inserter (to simulate the super-fast inserters used by miniloader) picking up from that single low speed belt (and into a chest or something).
Basically the moment the item moves onto the low-speed section the inserter picks it up and moves it away, allowing for the next item to move onto the low-speed section regardless of the actual speed of the low-speed section.
The solution seems to be to set up the rotational speed of the hidden inserters such that at each tech level they are just a bit faster than required to pick up a full throughput of the correct tech-level belt (and naturally allow for only stack size of 1). Alternatively if the mini-loader is changed to be 2 units long (as with the vanilla loaders) you could ensure that both of the 'internal' belts are of the proper speed. As inserters seem to pick up from the grid position, moving them 'back' away from the input belt will not work.
