'Does that mean that Apple's 10.4.6 Combo Updater for Intel is actually a Universal Binary that will update a PowerPC as well?' - no. 'Mac OS X 10.4.6 Combo for Intel' is strictly for Intel based Macs. 'Mac OS X 10.4.6 Combo for PPC' is strictly for PowerPC based Mac's.
Believe it or not - I read the post and went down a path I should not have.
Thus for clarity, and actually answering the original post of 'Why are Mac OS X for Intel updates larger', - when code is compiled for different microprocessors - the resultant code size will vary.
Thus, assuming that only the same exact fixes were compiled for both processors - the resultant upgrades would most likely be of different sizes.
Also, the MacOS X update(s) for the Intel based Macs may include additional code, for whatever reason, by Apple. This is quite likely considering - that most of the code written for the PowerPC based Macs is quite mature, and any updates would be just that - updates. But, Apple is still fixing MacOS X to run on the Intel based Macs; thus, It is quite possible that additional fixes (tweaks) are also being included [in addition to the code being added to the PowerPC version of the update(s)] in the Intel update releases.