I presumed the Random selection was optional, but it may not be on a second reading. No idea how random selection of Qualities would work, especially at Step Four when you could actually be out of Karma to spend....
To your other points. My own suggestion was to count "Collectives" (p.117) as a separate cost paid at Step Four, like Metavariant/Metasapient Karma costs. And simply count Metagenic Qualities as Qualities. RAW Metagenic Qualities cost double, which is likely not intended. RAW, Metagenic Qualities are purchased at Step Four, Step Four says to use the Advancement Costs chart on p. 68, Advancement Chart on p. 68 says Qualities cost double. Which is 5th edition Ways all over again.
All on the (FAQ/Errata) list, thank you.