I've also tested this on the mac (10.15.7 Catalina) versions of Affinity Publisher beta v1.9.0.887 and Affinity Designer beta v1.9.0.9.
Pdf produced in QuarkXpress v13.0, pdf-version v1.4 and they have the same problem.
It appears the tracking on every hyphenated word gets screwed up when imported into either Publisher or Designer, but I guess they're both using the same pdf import code.
The document has been auto-hyphenated in QuarkXpress and after importing it in Publisher/Designer, around every hyphen, even the ones that look ok, the character tracking is a negative value varying between -300 down to -500.
There is also a mysterious extra space inserted before every hyphen character, like "BE -FORE". It will appear if you select the hyphenated word and set the tracking to zero.
Maybe that "space-hyphen" combination is used in Quark to mark that the word has been auto-hyphenated and then negative tracking is used to hide the extra space? Sounds a bit wild, but who knows?
Example: in the word "BE -\nFORE" the tracking values are zero except for the space and the paragraph break where they dive to -450.
Like this: "0,0,-450,0,-450,0,0,0,0".
You can easily produce the same "look" by typing some characters in a text frame in Publisher or Designer, selecting them and set the tracking to -450. They will overlap each other, which is the expected behaviour when setting crazy values.
The pdf I used as an example in my previous post displays correctly in Acrobat Reader so I assume either AR caps the tracking values if they're too low or they get screwed up in Publishers/Designers import code?