It should be fine, but you probably have to set
-k 200, similarly to what the TEToolkit manual suggests for STAR.
edit: I didn't see you already mapped the reads. Check the settings, the issue is, as you are trying to quantify features with potentially hundreds of copies in the genome, you want to be sure the aligned is considering them. STAR, by default, considers as unmapped reads mapping to more than 20 locations, hence you have to provide an additional parameter when you want to ten TEToolkit downstream. You should check how HISAT2 works in this regard, I am not familiar with it.