One thing we need to be always careful of is making sure our theories are supported with fact. As you mentioned, the earliest record we have of the MacDonald Lord of the Isles Hunting tartan is in the Vestiarium Scoticum, which was published in 1845. That book, though the Sobieski Stuarts claimed it to be a copy of a sixteenth century manuscript, later was shown to be a hoax. While some of the tartans included in that book have proven to be copies of extant tartans, many were seemingly created by the Sobieski Stuarts themselves. So, unless we find an earlier example of this MacDonald tartan, the safe assumption is that it was created by the Sobieski Stuarts.

The MacKenzie tartan, on the other hand, was created for the Seaforth Regiment that was raised by the Earl of Seaforth in 1778. As you have correctly pointed out, it is based on the Black Watch tartan (aka Government Sett). This is, in fact, a common origin for many regimental tartans. The Black Watch sett was used as the basis for the design and various colors were added to it.

Other tartans fitting into this category would include Gordon, Lamont, Robertson (Htg), Baillie, Farquharson, MacNab, Fraser of Lovat, MacLachlan, and many others.

The fact that many of these tartans came to be later regarded as clan tartans was because of the very close association between the regiment and the clan. Thus the tartan worn by the Black Watch regiment came to be worn by the Campbells, Munros, and Grants. The tartan worn by the Gordon Highlanders came to be worn by the Gordon clan. The tartan worn by the Seaforth Regiment became associated with the MacKenzies. The tartan worn by the Loyal Clan DOnnachie Volunteers was associated with the Robertsons. And so on...

So it falls well within the established tradition that the Seaforth regiment would wear a tartan that was based on the Government Sett with colored lines added for differentiation, and that tartan would later be regarded as a Clan MacKenzie tartan.

For the MacKenzie tartan to be based upon an older MacDonald "district" tartan, we would first have to establish that such a district tartan actually existed. That has not been done.

These two tartans do appear similar in terms of color, and some of the elements of the design. But we also have to keep in mind that this particular color combination is not that atypical of tartans in general, so it's probably best not to read too much into the similarities unless there is other evidence that would back up a connection.