(...so, I guess someone will have a problem with the following, then...)
I started messing about with some of the Universegen configuration settings. And now I know why "Expansion" is generally set to be a value of 2.0 or greater (you have to edit the configs to use lesser values, and even then you get something similar to an Embark Warning, for those that don't already know)... When you set the matter/anti-matter ratio to equal and there is a universal expansion of only 1.0 in the early times, you end up with a radiation-rich universe with virtually no structure left to it. Well, you've seen how frustrating that is.
With your Expansion set to the recommended levels (or higher), equal matter/anti-matter ratios cause an enormous amount of chaos, yes, but you get symmetry breaking at local levels so that significant regions of creation end up primarily of either one or the other type, and with the Expansion set to a 'reasonable' (i.e. allowed) value you find stable areas of universe that are sufficiently in the centre of one or other zone of polarisation that the inevitable matter/anti-matter interface effects are actually beyond the effective event horizon of these central areas, and leaves these areas (which you'll have noted are where the stable embarks lie) experiencing an observable universe of pretty much only matter (or anti-matter; but as has already been pointed out by others, this is normalised to be termed matter, in anti-matter-rich universegens, with the rare incidents of matter being renamed as anti-... and this is as true for a stable zone embark in a patchwork universe). The remnants of the early annihilation of course get interpreted as the CBR by your primitive society, also influencing their underestimated ideas of the age of the universe.
Beware, though, because if/when you get spontaneous wormholes between zones... well, it's not pretty. (Probably why some of us can find a lot of Region Rejects when setting Spacial Pliability too high.) Buffering with exotic and 'dark' particles and energies helps, though.
Oh yeah, and breaking the nominally coded upper limit on Expansion does (as already revealed in that other thread) tear the whole of creation apart before coalescence of anything habitable, normally. Although loading the Big Bang with enough extra energy might get you enough spontaneous energy->mass conversion to populate it with a lot of early activity (singularities will abound, though), if you carefully fiddle with some of the other parameters as well. I can't hand-hold you through that, though, because I'm my preferred end-result is a bit more flat and boring than the common consensus, in the first place.
(Oh yeah, I think I have got a handle on what sparks those occasional inter-planetary sieges. When a planet's inhabitants search for the mythical Higgs, but accidentally get the thing they'll eventually (and equally erroneously) call the supersymmetric Shiggs boson, first, their experiment sends a detectable superluminal ripple that seems to attract the nasties. As far as I can tell, you can't actually guide your charges towards getting the safer (and perhaps repellent?) version first, but I'm not sure whether this is hard-coded randomness or just something remotely connected with the above matter-polarity normalisation and other embark choices.)