It is not uncommon for a TCP packet to be modified somewhere in the path. There are many devices that proxy or regulate TCP traffic. Whether that might cause a problem for an algorithm that is measuring delays versus TCP windows would be a different story. If this algorithm also makes the mistake that nothing will modify a TCP packet, then likely it will not function properly in these cases.
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It is not uncommon for a TCP packet to be modified somewhere in the path. There are many devices that proxy or regulate TCP traffic. Whether that might cause a problem for an algorithm that is measuring delays versus TCP windows would be a different story. If this algorithm also makes the mistake that nothing will modify a TCP packet, then likely it will not function properly in these cases.