In defense of #1, I've read that retrotransposons can be irrelevant to the function of the cell. they survive random mutations through making more copies of themselves, so mutations will select for retrotransposons that A) increase their number of copies and B) don't harm the fitness of the host. they don't need to actually benefit the host to survive selection pressure. if they do, that's gravy.

I suppose they could also survive selection pressure by hurting the organism if they're not expressed. for instance, by capturing a vital protein-coding gene from the host, and arranging things so the transposon must stay active for the gene to be transcribed.