Your reply made me think of something I wanted to look up. I came across this:. https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1577-z#ref-CR27
TEs occupy a substantial portion of the genome of a species, including a large fraction of the DNA unique to that species. In maize, where Barbara McClintock did her seminal work [28], an astonishing 60 to 70% of the genome is comprised of LTR retrotransposons, many of which are unique to this species or its close wild relatives, but the less prevalent DNA transposons are currently the most active and mutagenic [29,30,31,32] (Fig. 2). Similarly, the vast majority of TE insertions in Drosophila melanogaster are absent at the orthologous site in its closest relative D. simulans (and vice versa), and most are not fixed in the population [33, 34]. Many TE families are still actively transposing and the process is highly mutagenic; more than half of all known phenotypic mutants of D. melanogaster isolated in the laboratory are caused by spontaneous insertions of a wide variety of TEs [35]. Transposition events are also common and mutagenic in laboratory mice, where ongoing activity of several families of LTR elements are responsible for 10–15% of all inherited mutant phenotypes [36]. This contribution of TEs to genetic diversity may be underestimated, as TEs can be more active when organisms are under stress, such as in their natural environment [37, 38].
When I said this
I didn’t realize that it was known that there are huge TE differences between species or close relatives in all kinds of eukaryotes.
I see your point here now especially, but TE differences is definitely something I’m interested now in paying attention to, to see if any patterns like with the salamanders come up in the literature.
I guess I didn’t let this thread die. 
I’ll see if I have more questions after I finish reading that paper/article.