Well you are right that if the storage isn't high enough, fast-charging would fail totally. I don't know if it's currently possible to drain energy from multiple sources at once, but if it was, setting the buffer to packetsize*16 (16x the maximum overclocker rate, or isn't it?), should work (it would result in 512,2048 and 8192 storage sizes, which still fine), while it would require the engineer to provide the energy in real-time (as other machine do when highly overclocked)
I don't think of the HV bench as "stealing" 10 million EU that you'll never see again. I see it as storing 10 million EU so it's ready to recharge that suit of quantum armor, nano armor, or other tools. It's not wasting EU sitting there, it doesn't ask for more from the Energy Net than it can take in and it never uses any EU unless it's actually charging an item. If you don't put any overclockers into it it won't waste a single EU of power. Anything that goes into the charging bench will come back out into items placed into it to charge. The faster charge rates and the ability to charge up to 12 items at a time absolutely require a sizable internal buffer of energy because it simply isn't practical to supply it with the kind of input needed in real time.
That depends on how much energy you operate with. If I ran a nuclear reactor, it's no problem to just fill it up and then recharge at will. Lately I tend to play with low-energy setups, running just several machines and basic tools, I would never use up 10 million energy on tools... not in the entire lifetime (we restart worlds relativelly often).
On the other hand, both LV and MV benches store relatively little energy, considering what one might want to charge (40k vs 60k batpack, 600k vs 200+300 laser+LP), the only problem is the HV bench. (Which I never use, so you can propably ignore my entire suggestion :))
However, it could still be useful if it was cheaper... That way, one could charge items, as fast as he can provide energy in real-time. That, of course, would be much weaker than the current charging bench, as it wouldn't be able to charge more than one item with no overclockers. However as this is quite a balance-changing feature, it would be up to you if you wanted to implement it.