Yes, reverse transcriptase is used by retrotransposons and retroviruses. There is a huge literature on the evolutionary genetics of transposable elements, and perhaps someone else has the time to summarize the key points. But I will note that as far as the effects, one can see thousands of processed pseudogenes in the human genome (derived from reverse transcription of mature mRNAs) and tens of thousands of remnants of endogenous retroviruses.

In plants at least, there have been large expansions of transposons in some lineages, which, arguably, have led to reproductive isolation associated with speciation. For instance, in Brassica, there are three generally accepted diploid genome karyotypes, AA, BB and CC, of which the C genome is much larger, physically. This large size is associated with large-scale proliferation of a C-genome-specific transposable element BoT1.

This is our paper on BoT1: https://www.researchgate.net/publication/23231177_The_CACTA_transposon_Bot1_played_a_major_role_in_Brassica_genome_divergence_and_gene_proliferation?ev=prf_pub

Generally, plant genomes tend to apply methylation to the regions of the genome dominated by copies of transposable elements, in order to prevent them being expressed, and thus potentially disrupting normal function. However, this methylation is obviously release from time to time to allow transposition, and there are reports that immediately after a polyploidy event, there can be explosions of transposition activity, but I guess here it could be argued that the polyploidy event is more relevant to reproductive isolation than the transposition per se..

Article The CACTA transposon Bot1 played a major role in Brassica ge...