After taking some tries with mapillary_tools for batch processing and upload I ended up with doing most sensitive part of geotagging manually (using exiftool)
Since gpx tracks in osmand do not capture directions (course/heading) - this needs to be interpolated and added during processing.
I have tried some tests and discovered that for some odd reason directions are not interpolated/written under certain scenario
mapillary_tools process --advanced --import_path "path_to_images" --user_name "user_name" --interpolate_directions
DOES NOT interpolate directions based on exisiting GPS Exif tags
mapillary_tools process --advanced --import_path "path_to_images" --user_name "user_name" **--geotag_source "gpx" --geotag_source_path "path/to/track"** --interpolate_directions
Difference between 1 and 2 is that in case 1 no geotagging is applied by MT, existing tags are used;
in case 2 - mapillary_tools are doing geotagging from gpx track themselves (even if GPS Exif already present)
Looking at the documentation I guess this is not an expected behavior and --interpolate_directions option should be working in both cases.