This definitely seems like déjà vu. I think I submitted this ages ago along with some other issues or general bad practices with the installer. And I agree, this is something the vendor should fix to preserve the signing. Ideally, they’d also make it more flexible for advanced workflows by supporting customizations or other components to be bootstrapped without re-packaging.
I’m currently dropping the unmodified BigFix PKG, the masthead, and a clientsettings.cfg into a parent PKG as script resources. I have to sign and notarize my PKG, but not HCL’s.
They already provide some of this with the clientsettings.cfg. Were you looking for more?
Honestly, the degree to which I am irked simply by the “Make Application directory what we need it to be” comment in the snippet I posted above (which “makes” nothing, just checks and exits) is probably unhealthy.
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Well, the fact that the BigFix downloads are categorized as Windows and “Non-Windows” might be a slight indication of where the platform priorities are. 
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