Signed Mac Apps – error message

TL;DR It's up to the developer to pick which pieces of the app are signed and whether or not tampering with those pieces results in any actions when the app is launched. You have to use trial and error to figure it out on an app-by-app basis.

It is largely up to the developer to decide which components in their application bundle are represented in the seal that gets signed before they deliver their application. Anything in the seal is effectively tamper-proof as it's mostly impossible to modify these things without changing their hash signatures. But that's doesn't actually mean you can't tamper with them.

The Apple Developer guide has this to say about what you should sign:

You should sign every executable in your product, including applications, tools, hidden helper tools, utilities and so forth. Signing an application bundle covers its resources, but not its subcomponents such as tools and sub-bundles. Each of these must be signed independently.

If your application consists of a big UI part with one or more little helper tools that try to present a single face to the user, you can make them indistinguishable to code signing by giving them all the exact same code signing identifier. (You can do that by making sure that they all have the same CFBundleIdentifier value in their Info.plist, or by using the -i option in the codesign command, to assign the same identifier.) In that case, all your program components have access to the same keychain items and validate as the same program. Do this only if the programs involved are truly meant to form a single entity, with no distinctions made.

A universal binary (bundle or tool) automatically has individual signatures applied to each architecture component. These are independent, and usually only the native architecture on the end user's system is verified.

In the case of installer packages (.pkg and .mpkg bundles), everything is implicitly signed: The CPIO archive containing the payload, the CPIO archive containing install scripts, and the bill of materials (BOM) each have a hash recorded in the XAR header, and that header in turn is signed. Therefore, if you modify an install script (for example) after the package has been signed, the signature will be invalid.

You may also want to sign your plug-ins and libraries. Although this is not currently required, it will be in the future, and there is no disadvantage to having signatures on these components.

Depending on the situation, codesign may add to your Mach-O executable file, add extended attributes to it, or create new files in your bundle's Contents directory. None of your other files is modified.

Also from here it's not necessarily true that having an invalid signature for an application means it will fail to launch. The page says:

It is up to the system or program that is launching or loading signed code to decide whether to verify the signature and, if it does, to determine how to evaluate the results of that verification.

An application may choose to allow modifications.

Your best bet is a trial-and-error approach with any application you're trying to modify. It may work, it may not. There's no always-true answer that can be given.

If an app has been signed you can look for a Contents/CodeResources file or a Contents/_CodeSignature/CodeResources file in the bundle. This file lists all the signed components and their expected hash values in the bundle. It's a good place to start understanding what pieces of the application a developer deems critical enough to watch for changes.

Yes, it's possible. Apps can be installed from multiple enterprise locations on the same device. Whilst I haven't been able to find a citable source, I have personal experience as I have apps from an enterprise organisation installed on my device as well as the SE iOS beta app which is distributed through enterprise.