I have several Orion-based PWAs installed on my main desktop system, running MacOS Sequoia 15.6.1. All PWAs were installed prior to to the Orion v1.0 update. I really like the option to install PWAs for frequently-used webapps, thanks for making this feature. I use just one profile in Orion normally, but have two that are active (the second one has nothing in it currently).
Since the Orion v1.0 update, any external link clicked in a PWA (any PWA, I have tried them all) opens in a new instance of Orion — not just a new window (which would be annoying too since I have a preference to open all links in new tabs, not new windows), but a new dock icon in my main profile.
My Orions after clicking some links from a PWA (RSS reader in this case):

Right-clicking PWA links and choosing any option ("Open Link," "Open LInk in New Tab," "Open in New Window") does the same behavior described here. "Open Link in New Private Window" does the same too, but the window is indeed private.
I would expect a link clicked in a PWA to open the link in a new tab in the active instance of Orion (my default browser) rather than in a new instance of the browser every time. This is exactly how PWAs worked prior to Orion v1.0, so I'm not sure what changed. I'd rather not have to reinstall these PWAs as some of them have a lot of stored data and it would be time-consuming to start from scratch.
Thanks for taking a look!
Version 1.0.0 (139), WebKit 623.1.8.0.0
Sequoia (15)