Hi Trident1. Before you get into rechargeable Li-ion cells, I strongly recommend you read up on the relevant threads in
the sticky and the
Smoke and Fire sub forum at the top of this forum. Also, you will need a means to measure the voltage of your Li-Ion cells, such as a DMM. This is pretty much mandatory when dealing with Li-Ion cells. Your choices as to charger and cells are a couple of the best, no problem there.
- for least hassle and safety, I go with protected ony?
Yes, particularly when using cells in series applications, protected cells are the only way to go. Until you become familiar with Li-Ions, protected cells are best for all applications.
what's plus/minus of IMR batteries (the MAC's custom I'm looking at requires it)
IMR cells are a "safer" (note, I said "safer", not "safe") chemistry than LiCo cells. Their only drawback is that they have lower capacity when used at low current rates. The reverse is true at very high current rates such as in your Mac's custom.
The only difference here, is that in some lights, flat tops may not make a good connection (or none at all) in the light due to not having a protruding nipple. In some rare applications, flat tops are better because they are often a mm or so shorter.
do I need to buy spacers for different batteries?
This all depends on whether you need them, or not..........

OK, seriously, I'm not sure what you mean here. For charging cells other than those that are ~65mm (eg. 18
650, 17
650 etc.), or ~50mm (17
500, 14
500 etc.) long in the Pila, you will need additional spacers, or some sort of adapter to charge these cells. As for using spacers in lights, this is rarely necessary.
will the basic Pila charger work for rechargables of different sizes(AAA,AA, as well as the CR123 variants)?
The Pila will work for most Li-Ion cells of LiCo, or LiMn chemistry that have a capacity of 600mAh, or more. It is not recommended for LiCo cells of less than 600mAh capacity, as the charge current is too high. This means for cells such as RCR2 (15270), 14250, or 10440 (AAA), you will need another charger.
Kinda quick, but I hope this helps. Again, please do read through the threads in the links I provided.
Dave