Run some custom code after execute, but before application exit

So basically, I have an app that modifies the registry at run time which breaks portability unless I rewrite it after the fact. I've hacked together two approaches - one using a bat script to launch the app, sleep, and then rewrite the registry, and one using OverrideExecute. It's just a slightly modified version of execute block from the launcher source. The bat file is basically the same thing.

${SegmentFile}

Var URLCommand

${OverrideExecute}
    ${!getdebug}
    !ifdef DEBUG
        ${If} $WaitForProgram != false
            ${DebugMsg} "About to execute the following string and wait till it's done: $ExecString"
        ${Else}
            ${DebugMsg} "About to execute the following string and finish: $ExecString"
        ${EndIf}
    !endif
    ${EmptyWorkingSet}
    ClearErrors
    ${ReadLauncherConfig} $0 Launch HideCommandLineWindow
    ${If} $0 == true
        ; TODO: do this without a plug-in or at least some way it won't wait with secondary
        ExecDos::exec $ExecString
        Pop $0
    ${Else}
        ${IfNot} ${Errors}
        ${AndIf} $0 != false
            ${InvalidValueError} [Launch]:HideCommandLineWindow $0
        ${EndIf}
        ; There's probably a reason ExecWait was used here, but that prevents us from running things post exec but before the program has terminated
        ; The loop gated by WaitForProgram below seems to accomplish the same thing.
        ; In this case, we need to update the registry post exec, as the binary updates the registry at run time
        Exec $ExecString
    ${EndIf}
    ${DebugMsg} "$ExecString has finished."

    sleep 100

    ; TODO: make sure the program is still running (not a huge risk if sleep time is small)

    StrCpy $URLCommand "%PAL:PortableAppsDir%\ObsidianPortable\ObsidianPortable.exe"
    ${ParseLocations} $URLCommand
    ${registry::Write} "HKCU\Software\Classes\obsidian\shell\open\command" "" "$URLCommand %1" "REG_SZ" $0
    ${DebugMsg} "Attempted to write to registry, operation returned $0"


    ${If} $WaitForProgram != false
        ; Wait till it's done
        ClearErrors
        ${ReadLauncherConfig} $0 Launch WaitForOtherInstances
        ${If} $0 == true
        ${OrIf} ${Errors}
            ${GetFileName} $ProgramExecutable $1
            ${DebugMsg} "Waiting till any other instances of $1 and any [Launch]:WaitForEXE[N] values are finished."
            ${EmptyWorkingSet}
            ${Do}
                ${ProcessWaitClose} $1 -1 $R9
                ${IfThen} $R9 > 0 ${|} ${Continue} ${|}
                StrCpy $0 1
                ${Do}
                    ClearErrors
                    ${ReadLauncherConfig} $2 Launch WaitForEXE$0
                    ${IfThen} ${Errors} ${|} ${ExitDo} ${|}
                    ${ProcessWaitClose} $2 -1 $R9
                    ${IfThen} $R9 > 0 ${|} ${ExitDo} ${|}
                    IntOp $0 $0 + 1
                ${Loop}
            ${LoopWhile} $R9 > 0
            ${DebugMsg} "All instances are finished."
        ${ElseIf} $0 != false
            ${InvalidValueError} [Launch]:WaitForOtherInstances $0
        ${EndIf}
    ${EndIf}
!macroend

My question is, is there a supported way to do this that I missed?

As an aside, it's my understanding that associations are horribly broken by win 8/10, but it seems that the user choice dialog is only triggered in certain flows - triggering url associations from within the app doesn't bring up the user choice dialog, it just works. The application needs a url association to open files in a different vault (vaults are just folders)