I had some trouble with the title for this one, but a plot should explain:

alTrack <- Gviz::AlignmentsTrack(
  system.file(package = "Gviz", "extdata", "gapped.bam"),
  isPaired = TRUE)

alTrackHighlight <- Gviz::HighlightTrack(
  trackList = alTrack,
  start = 3048600,
  end = 3048700,
  chromosome = "chr12")
Gviz::displayPars(alTrackHighlight) <- list(
  fill = "green",
  col = "transparent"
)

res <- Gviz::plotTracks(
  alTrackHighlight,
  from = 3048500,
  to = 3049000,
  type = c("coverage", "sashimi", "pileup"),
  chromosome = "chr12"
)

Is there a way I can tell the highlighted region to be added "on top of" the coverage histogram, just like it is "on top of" the reads below?

I think that you'd have to add transparency to the coverage histogram. HighlightTracks always sit behind the drawing canvas. The only reason why it appears to be above the reads is because they also use transparent colours. I don't think that we are exposing the alpha level for the histogram, though. If you just want constancy, you could set alpha.read=1

That would remove the transparency from the reads.