By digital charger we are assuming you mean our charger or Reliacharger. 

Yes the charger will time out on a 4800 most of the time, especially if the 4800 is really depleted. What we recommend you do is, put your 4800 on charge after an hour of charging come back to the Reliacharger and Rock the Rockerswitch, this will reset the timer.  You do not have to pull the batteries off the charger to do this, it can be done while a charge is taking place. The switch controls the both the Rate of charge and the 3 hour safety timer.

On the 3S 2500 pack, the Super Reliacharger only charges 2S or 7.4volts, so yes you will have some problems here with not getting even close to a full charge.

If I charge my 2400 Relions using the 2A setting, after the green light goes out can I set the toggle switch to the 1/2A setting and let it go until the green light goes out? I want to top off the packs after the 2A charge is done.

That's right.  The charger's green light goes out when current reaches 100mA on the 2A setting, and 25mA on the 1/2A setting (C/20).  Selecting "1/2A" to do a topping charge works well.

The charger does continue to charge at a low rate for about 45 minutes after the green light goes out, as well.  There's no indication, though. The green light going out is intended mainly to be a "full-enough-to-fly" indicator, and represents about 92% of charge.

Please be aware that the charger also has a timer; charger will turn off after 3 hours whether the battery is full or not (safety feature).

Can I charge Li-POLY as well as Li-ION batteries with the reliacharger?  OR is there a multi-output charger that will charge both types of cells?

Yes Lipoly packs can be charged on our chargers.  The Reliacharger will only charge 2S or 2cell packs, as long as that is taken into consideration, then yes go for it.