This is also what I think about this issue.
(...) was the unfinished Fuge intended to become a part of the Art of the Fugue?
I tend the most to believe, that the AoF is complete without it, and that Bach had not planned more Contrapuncti than the seventeen we know. He was preparing the AoF for publication in the last days of his life, and he probably knew, that he only had a short time left, so why should he use energy to write another Fugue with no relation to the AoF? The answer is probably, that the AoF was complete already.
If we on the other hand suppose, that the Fugue á 4 was intended to become Contrapunctus XIV of the AoF, this may explain why he worked with it at that time.
But if it was intended to become a part of the AoF I find the theory about the quadruple Fugue (the main theme combined with the three themes of the unfinished Fugue) ridiculous. Bach would rather have concluded the triple Fugue with some further combinations of the three established themes, and maybe he later would have written another triple Fugue combining the BACH theme with the main them of the AoF and maybe the second theme of the unfinished Fugue, which combines well. And maybe later he would have written a quadruple Fugue with these three themes and a new fourth theme or maybe a theme derived from some of the earlier Contrapuncti. Like you I find the first theme of the unfinished Fugue too similar to the main theme of the AoF, making the combination of these two themes unlikely, as far as I know Bach's working principles and artistic self demands.
Regards,