There should be no problem with partial charging lipos. I regularly charge to only 90%-95% a pair of Trakpower bricks with no problems.
The mah setting on the hyperion charger will only effect the current rate that the pack is charged at. I have a couple of the evolite packs that I charge at 50mah over which causes no problems either. Either way you will get a full charge unless you end it early.
with the hyperion chargers, in the owners manual it says to charge the 4350 mah packs (for example) at 4400mah. it will not harm the battery. i personally love my eos1210i.