"Star Raiders" is a 12 KB game. This matches with the chip sizes that you've found - the cartridge contains one 64 Kbit = 8 KB and one 32 Kbit = 4 KB chip, which sums up to 12 KB.
What bugs me, these two cartridges contain chips with differing internal part numbers. That most certainly means that the contents of the ROMs also differ.
I've cross-referenced the numbers with Atari's "Engineering Information System - Item Master List". Here are all the pages with part numbers for 5200 ROMs:
The ROMs from the "25 3 R" cartridge are described there as "CX5205 CARTRIDGE" while the "29 3 PR" ones are described as "CX5205P CARTRIDGE". Considering that, in the context of this list, the "P" in description of 2600 cartridges means PAL variants, this would mean that the "29 3 PR" cartridge indeed contains an updated version of "Star Raiders", modified to support the planned PAL 5200 console. There exists a PAL prototype of Star Raiders, so maybe they simply replaced the original release with the PAL-compatible version at some point in time?
Look, there are several other ROMs listed as "CX52xxP CARTRIDGE". There may be more game revisions in the wild that we don't yet know of. I guess we need a coordinated effort to search for and dump the 5200 cartridges like we started in the 8-bit section a few years ago.