I've settled on a solution to the galaxy scale mismatch discussed in the previous post.
I analyzed the Mikesh map and, while the horizontal/vertical parsec ratio is only 0.9, that's closer to the actual ratio than 1.0 which is the ratio of the Linehan map.
So I've decided to keep the Mikesh map as the primary data source. The galactic structure is now scaled to fit it, which means the Galactic Rifts line up. The change is subtle enough to be pretty much unnoticeable unless you zoom in to where the Core Route and the Galactic Rifts line up - then they are off by several sectors. But honestly, these were wonky anyway.
BeRKA suggested dropping some of the Core Route sectors, but they actually have route metadata winding through them. Honestly, I think they're mostly just a "cute" addition to the site and don't take them particularly seriously, but enjoy having them. So I might as well keep them intact.
By the way, the horizontal/vertical parsec ratio is noticable in Classic Traveller material as well. If you compare the shape of the Imperium presented in the Atlas of the Imperium (by, say, photocopying each page and laying it out like a poster... not that I ever did that...) with the shape of the Imperium as presented in the Alien Module maps you'll see that it's "squashed" in AotI. This is because the AotI-style maps use square hexes. The "Atlas"-style rendering on the site uses rectangular hexes. I believe this "squashing" infected the DGP dotmaps as well (in Vilani & Vargr and Solomani & Aslan).