The sequences we're discussing aren't really random, though. Presumably the chance of viability with such a sequence incorporated, though still low, is much higher than if it were a truly random sequence.
Having one foreign sequence which have some specific features (to keep the originating organism viable) could have a chance of never being compatible with the target organism.
Having a completely random sequence by definition have some chance of being compatible.
The question is which scenario has a higher chance of success.
This is a case I could see going either way. Random mutations are probably much smaller and closer to the original, and therefore potentially more viable. Yes, it's random, but most of the time it won't have a major effect on the proteins the DNA generates. On the other hand, if we are talking about transferring segments, there's the potential of that DNA to create actively harmful proteins.
