brent I'm confident there's no risk in updating for you, since I have the same kind of setup where I have an nvidia Flatpak installed, even if I have already the system nvidia drivers. See here:
↪ flatpak list
Name Application ID Version Branch Installation
Microsoft Teams com.microsoft.Teams 1.3.00.30857 stable system
Freedesktop Platform org.freedesktop.Platform 20.08.3 20.08 system
default org.freedesktop.Platform.GL.default 20.08 system
nvidia-460-39 org.freedesktop.Platform.GL.nvidia-460-39 1.4 system
Intel org.freedesktop.Platform.VAAPI.Intel 20.08 system
openh264 org.freedesktop.Platform.openh264 2.1.0 2.0 system
Plata theme noir org.gtk.Gtk3theme.Plata-Noir 3.22 system
Zotero org.zotero.Zotero 5.0.95.3 stable system
Zoom us.zoom.Zoom 5.5.6981.0202 stable system
↪ eopkg info nvidia-glx-driver-current
Installed package:
Name : nvidia-glx-driver-current, version: 460.39, release: 367
Summary : NVIDIA Binary Driver (Current Kernel)
Description : NVIDIA Binary Driver (Current Kernel)
Licenses : EULA
Component : kernel.drivers
Dependencies : linux-current nvidia-glx-driver-common
Distribution : Solus, Dist. Release: 1
Architecture : x86_64, Installed Size: 43.30 MB
Reverse Dependencies:
As to whether Flatpak should be able to detect the system drivers and interact directly with them, I don't know enough to give an informed opinion.
Is a Flatpak just programmed to ignore the architecture it's installed on? Agnositc and unaware? Independent? That simple?
I think you're hitting the nail on the head here. Flatpak are cross-platform, so I personally never worried about seeing an nvidia package prior to your post because I just assumed they were installed in order not to rely on the underlying system.