I have been very tempted to comment that you are all overthinking this.
Without a doubt.
why didn't they just make humanoids?
It does appear logical to me, sort of. These Progenitor folks supposedly began their galactic seeding program because they felt their own mortality catching up on them. They were lonely, they knew they'd go extinct one day, they wanted to leave a monument in form of some sort of offspring, and they didn't want this offspring to be as lonely as they had been.
Really, it strikes me that a sapient species with the capabilities of the ancient humanoids is probably the least likely one in the whole galaxy to die out. It is far more likely that their untended experiments would go disastrously awry--as it surely did, many times, on Earth, unless it was all part of their plan, and they accurately predicted the late heavy bombardment, and the P-T and K-T extinctions amongst others, which is bewilderingly
Given this, I wonder if the Progenitors and Battlestar Galactica's God are the same people. They both go to insane lengths to accomplish very questionable goals.
It also seems very unlikely that you can code humanity into a prokaryote, which were probably the only thing that would have existed when the progenitors were doing their thing, at all. Even if you could, surely it would have been noticed very rapidly that the staggering amounts of junk DNA in virtually every life form on every planet visited by the progenitors coded the same information as what is likely to have been the most studied DNA on any of those planets, that of the humanoid being.
There is also a question of physical possibility of the progenitors' carbon-based evolution beginning perhaps as far back as nine to ten billion years ago. Astrophysically speaking, that long ago, did sufficient concentrations of carbon, nitrogen, oxygen and other materials vital for life-as-we-know-it exist?