update Apps will be easy without rebuild boot. wim, so good for testing.
Yes we do similar with the same reasons.

(difference: search for a special .cmd file to start at boot)
I wrote info to my home "WimBuilder Help 2"

*
I believe the time to inform things related to RunFrom ...
For now I use Plugins with only the option to add boot.wim , boot.wim file size gets bigger.
Since WimBuilder do not have much App patches for now (packages .. for now I continue saying patch, let me know when you decide a name change)
eg.
Customize-Apps\"7-zip" Patch add to boot.wim , no option on 7-zip Patch to add to cd (iso)
----> When number of WimBuilder App Patches increase, you will get Boot.wim size troubles
on my side, 7-zip plugin have options with RunFrom ( Apps\File Tasks\Compression\"7-Zip File Manager" plugin )
Run From Normal do nothing but only follows default Project settings (Normal)
--> To me WimBuilder current default Project setting is Ram (boot.wim)
--> Win10PE SE default Project setting is iso (RAM)
Run From RAM add to boot.wim
Run From CD add to iso
Shortly on my side, App Plugins Normally add to cd without getting boot.wim bigger.

To get things work, we use a
dirty solution that fits MOST users, at boot time before shell, change drive letter to Y:
* Dirty Solution :
How RunFrom macro works:
RunFrom,Ram changes 2 variables till the end of the plugin.
%Target_Prog% = %TargetDir%\Program Files
%PE_Programs% = X:\Program Files
RunFrom,CD changes 2 variables till the end of the plugin,
on SE :
%Target_Prog% = %TargetFinalDirr%\Programs
%PE_Programs% = Y:\Programs
on LiveSystemPro (Win7PE - Win8PE - Win10PE)
%Target_Prog% = %TargetFinalDir%\Program Files
%PE_Programs% = Y:\Program Files
reminding, Since RunFrom,CD is default (normal) setting, all Apps plugins work without using RunFrom macro all goes to cd.
ps: %PE_Programs% used to add registry and to create shortcut
* Why Dirty:
If cd drive not available for any reason, pxe boot most popular reason, registry + shortcut will not work ........
* Clean Solution:
I remember VistaPE times Nightman tried to provide a clean solution but not finished, later since Dirty solution was easy to implement things goes that way ...
When you decide to implement RunFrom options, IF you do not want to spend much time, use Dirty solution, It will work and will be quick.

On my side,
If you only add a BeforeShell task to change cd drive letter to Y: , I can quickly get Plugins add to cd as default (for now to boot.wim as default following WimBuilder)
and
On your side,
It will be easy too.
* If more time here is the Clean one:
RunFrom,CD changing location to
%Target_Prog% = %TargetFinalDirr%\Programs
%PE_Programs% = Y:\Programs
but also changing registry hive locations:
%RegSystem%= %TargetFinalDir%\PEMaterial\config\System
%RegSoftware%=%TargetFinalDir%\PEMaterial\config\Software
%RegDefault%=%TargetFinalDir%\PEMaterial\config\Default
%RegComponents%=%TargetFinalDir%\PEMaterial\config\Components
%RegDrivers%=%TargetFinalDir%\PEMaterial\config\Drivers
and also shortcut locations:
eg.
%TargetFinalDir%\PEMaterial\Shortcuts\Users\Default\Desktop"
%TargetFinalDir%\PEMaterial\Shortcuts\Users\Default\AppData\Roaming\Microsoft\Windows\Start Menu\
This way when WimBuilder Boots, Before shell:
After finding driver letter:
- change drive letter to Y: (Using Y: helps to write registry easier)
- add environmental variable %CDDrive%=Y: (helps to write .cmd easier ;))
- reg add hives at CD:\PEMaterial\config\....
- copy shortcuts at CD:\PEMaterial\Shortcuts\
- continue other CD:\PEMaterial\....
and all ready.

If cd fails (pxe boot), there will not be CD:\PEMaterial\config\.... no CD:\PEMaterial\Shortcuts\ , there will not be not working shortcuts or bad registry pointing to cd drive.
On my side, since using dirty solution, we ask end user change project setting to "Run All From Ram", so plugin default behaviour changed to always add to boot.wim
With Clean Solution, no need another special pxe boot iso.
Clean but requires a lot work, with small-time and no request I always postpone this idea for 10 years now ....

Tips:
Find drive letter: See Apps\System Tools\"Portable Finder Startup" plugin
add environmental variable %CDDrive% : See Utils\"BroadcastEnvChange.exe by Galapo" Plugin
change drive letter to Y: See Build\"CdDrive - X: - Y:" Plugin
******
Clean or Dirty or Have no interest or Have no time = All fine to me.

Reminding Above is not a request.
I have a good time testing and using WinBuilder2 with all inside Boot.wim

Only sharing some info and experience for your future development.

