Finally got round to working on this more (university side tracking me). I finally managed it and here is how I added syswow64 to a stock WinRE 10586 image. (Requires you to create a Win10PESE image with Wow64 basic)
Obviously full credit goes to everyone at The Oven/Win10PESE team, all I did was go back through their script. Thankyou to all who originally figured this out!
1) Mount your desired image, and delete \windows\syswow64 and \windows\winsxs
- Note you will probably need a program like Unlocker to delete them as they are very resistant to security options usually
2) After finishing deletion, copy in those folders from the Win10PESE image
3) Copy \windows\system32\catroot from your Win10PESE image and merge with the same folder in your target image
4) Copy hiderun.exe, setwow64.exe, wow64.dll, wow64cpu.dll and wow64win.dll from your Win10PESE image's \windows\system32 directory to your desired image
5) Set your winpeshl.ini to call setwow64.exe upon startup using hiderun.exe
6) Load \windows\system32\config\SOFTWARE hive from your desired image into regedit under the name tmp_software
7) Extract 10000_SxS reg file from 5-Wow64.script and run it - it will add everything to your tmp_software key.
8) Add the keys specified under the RegWrite section of the 5-Wow64 script
9) Load \windows\system32\config\SOFTWARE from your Win10PESE image under the name tmp_software2
10) And this is what I was missing before, export everything from your Win10PESE tmp_software2\microsoft\windows\currentversion\sidebyside to a reg file. Replace all tmp_software2 to tmp_software and then use this to add the keys to your desired image.
Haven't tested extensively but the three apps I've tried so far have worked beautifully, finally no side-by-side errors!
(also while I'm here - shellstyle.dll is causing memory read errors with open/save prompts, deleting it fixes this issue. But I need it for the file copy progress bar. Only happens in 10586 and not 10240, any ideas?)