My answer was provided by TLama (and Miral) in this question.
In the main application setup .iss, add a registry key with the app installation dir:
[Registry]
Root: HKLM; Subkey: "Software\Company\{#AppName}"; ValueType: string; ValueName: "InstallPath"; ValueData: "{app}"
And in the plugin .iss we simply use that key if it exists, and if not install to the default path:
[Setup]
DefaultDirName={reg:HKLM\Software\Company\{#AppName},InstallPath|{pf}\Company\{#AppName}}
DisableProgramGroupPage=yes
DirExistsWarning=no
In this example, I've also disabled adding program group in the start menu for the plugin, and suppressed the warning that we're installing to a non-empty dir (since the main app is already there that's always going to be true).
Additionally, this question has information on how the DefaultDirName can be changed dynamically through the [Code] section.