The code below:

transcriptID <- "ENST00000395443"

mart <- biomaRt::useMart(
  biomart = "ENSEMBL_MART_ENSEMBL",
  dataset = "hsapiens_gene_ensembl",
  host = "dec2013.archive.ensembl.org")

# Create transcript track
biomartTrack <- Gviz::BiomartGeneRegionTrack(
  filters = list(
    ensembl_transcript_id = transcriptID),
  biomart = mart)

# Create axis track
axisTrack <- Gviz::GenomeAxisTrack()
displayPars(axisTrack) <- list(
  add53 = TRUE,
  labelPos = "below",
  cex = 1.5
)

# works as expected
Gviz::plotTracks(
  c(biomartTrack, axisTrack),
  chromosome = "chr3")

Produces this plot:

And if I add reverseStrand=TRUE, I get this:

# add53 in same position?
Gviz::plotTracks(
  c(biomartTrack, axisTrack),
  chromosome = "chr3",
  reverseStrand = TRUE)

As you can see, everything is reversed except for the 5' and 3' indicators. As the arrows on the axis change, shouldn't the add53 parameter react to reverseStrand also? Or should I react to that by using add35 instead?

yes. 

And sorry for the late reply. I was a bit lazy recently with Gviz stuff. Will add it on the list of fixes.

Thanks

Looks like I forgot to commit this fix. Will become available shortly with Gviz 1.16.1 and 1.17.1