IO-540
You can't have an approved transponder installation with a PORTABLE battery - it's not certifyable. To certify the installation means showing that all component parts will remain in place to specified G loads - bits in the cockpit which can injure the occupants in an accident must be secure to 18G forwards. Hidden bits need to meet 9G (all details are in EASA CS23.561)
The Lithium battery problems with catching fire have long been recognised - hence they've not seen widespread use so far, other than memory back-ups in GPS systems and deployment batteries for ADELTS (helicopter deployable ELT's used on North Sea).
The new development in Li batteries is meant to address these issues and provide the opportunity for smaller, higher capacity batteries so you can run essential equipment e.g. transponders in non-electric aircraft. I've heard it mentioned from a battery manufacturer that the EU will ban production of Lead-Acid batteries from 2012 - will we go to Ni-Cad, with similar overheat problems, or to the new high-capacity Li. I think it'll be the latter, as we'll end up with more glass cockpits needing more power for continued operation when the generator fails.
On the different transponder units for height/speed ranges, certainly the Filser unit required a different altitude sensor to get the required 35000 feet, and it's got to maintain it's accuracy, so it's got to be pretty good, considering it's tiny space in the existing transponder case. Also, for both Filser and Becker, the output power is higher for the greater range requirements. As aviation product runs are much smaller that commercial electronics, I guess the manufacturers see this as a way to claw back some of the additional development and certification costs.