The offset is definitely the way to go. I opened the map, and re-saved it using csv instead of base64, so you can see how it's organizing the tiles. The file itself has no direction whatsoever of how to format the tiles, and pytmx doesn't help there, either.
I think what you want to do, is calculate how many tiles are in each row, which you can use to determine the offset (offset is based on the width of the tiles*number of tiles), and try to format it that way. I can't test it right now, but I'll try to try it out tonight.
The file:
<?xml version="1.0" encoding="UTF-8"?>
<map version="1.2" tiledversion="1.3.2" orientation="isometric" renderorder="left-down" compressionlevel="0" width="16" height="16" tilewidth="64" tileheight="32" infinite="0" nextlayerid="8" nextobjectid="1">
<tileset firstgid="1" source="outdoor pack.tsx"/>
<layer id="1" name="Ground" width="16" height="16">
<data encoding="csv">
11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,
11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,
11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,
11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,
11,11,11,11,11,11,11,11,11,11,11,11,31,11,11,11,
11,11,11,11,11,31,11,11,13,11,11,11,11,11,11,11,
11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,
11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,
11,11,11,11,11,11,11,11,11,11,11,31,11,11,11,11,
11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,
11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,
11,11,11,11,11,11,11,13,11,11,11,11,11,11,11,11,
11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,
11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,
11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,
11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11
</data>
</layer>
<layer id="2" name="Floor" width="16" height="16">
<data encoding="csv">
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0,0,0,0,175,175,175,175,175,175,175,175,0,0,0,0,
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</data>
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<layer id="3" name="M1" width="16" height="16">
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