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The reality is that PowerPC machines have, at most, perhaps 2% of the installed user base, and Linux on PowerPC is probably about 2-5% of that again (at most). That's 0.02 * 0.03 (let's say 3% of Mac users run Linux and be generous) which equals 0.0006 or a fraction of one percent of the installed user base.

Don't get me wrong. We'd like to support PowerPC, but it's hard because realistically very few software developers use Linux/Mac and therefore, few people would build PowerPC autopackages. There were discussions of cross-compilers and using LLVM as a virtual machine, but Apples announcement that they're dropping PPC for their consumer line (and probably in future for nearly everything else) has ensured that this is now way down the priority list.

It works well for the vast, vast majority of people who run Linux on x86 compatible systems.

Now, the 64 bit performance issue is much more valid. Some programs can gain a slight increase in computation speed because AMD64 has more registers, better support for PIC code and a few other nice things. Still, a few facts must be remembered:

Very few programs are CPU bound these days. Your average desktop application is IO bound (ie, disk speed). Generally what matters to desktop users is things like "how fast does my program start?" and "does running this program use up all my memory so pushing it into swap hell?". The 64 bit extensions don't matter for this common case.
For some apps, being 64 bit can actually slow them down as you double the size of every pointer, which makes your CPUs dcache a lot less effective (seeing as how pointers are very common things to store in memory). So it's not necessarily a win if you don't benefit from the CPU speed enhancements - it's for this reason that Apple are not porting the MacOS X APIs to be 64 bit: it'd be a net performance loss on PowerPC. For AMD64 it's a bit trickier because sometimes things get faster and sometimes they don't. But don't assume it's black and white.
Many games are GPU bound rather than CPU bound.

For the rare case of an app or game where 64 bit makes a noticable difference (things like audio/video editing apps would probably benefit) you can just provide two packages and let the user decide which they want.