Regression in 9.4.1: GHC compiles unreferenced `.hs-boot` files eagerly

As a regression over 9.2.4, GHC 9.4.1 reports missing home modules which exist in the source tree but are not referenced from anywhere.

To reproduce, unzip missing-home-modules.zip, change to the root folder there and run cabal build:

agda-missing$ cabal build -w ghc-9.4.1

<no location info>: error: [-Wmissing-home-modules, -Werror=missing-home-modules]
    These modules are needed for compilation but not listed in your .cabal file's other-modules: 
        Agda.Utils.Ord

(Note: there is also a script reproduce.sh with the failing GHC call, but this works only on my machine due to local package IDs. It is easy to extract such a script from cabal build -v3.)

(Downstream issue (cabal): https://github.com/haskell/cabal/issues/8367.)