Right - I've redone the retail install then patched to 1.20. It does not appear to make any material changes to the registry (i.e. some non-freespace2 parts of the registry files changed for some reason)
$ diff system.reg*
31908c31908
< [Software\\Microsoft\\Windows\\CurrentVersion\\Fonts] 1392808491
---
> [Software\\Microsoft\\Windows\\CurrentVersion\\Fonts] 1392808398
35597c35597
< [Software\\Microsoft\\Windows NT\\CurrentVersion\\Fonts] 1392808491
---
> [Software\\Microsoft\\Windows NT\\CurrentVersion\\Fonts] 1392808398
40559c40559
< [System\\CurrentControlSet\\Control\\Print\\Printers\\Brother-HL-2170W] 1392808493
---
> [System\\CurrentControlSet\\Control\\Print\\Printers\\Brother-HL-2170W] 1392808398
40586c40586
< [System\\CurrentControlSet\\Control\\Print\\Printers\\PDF] 1392808493
---
> [System\\CurrentControlSet\\Control\\Print\\Printers\\PDF] 1392808398
$
$ diff user.reg*
259,266d258
< [Software\\Microsoft\\Windows\\CurrentVersion\\Explorer\\Advanced] 1392808494
<
< [Software\\Microsoft\\Windows\\CurrentVersion\\Explorer\\ComDlg32\\LastVisitedMRU] 1392808496
< "a"=hex:73,00,65,00,74,00,75,00,70,00,2e,00,65,00,78,00,65,00,00,00,43,00,3a,\
< 00,5c,00,47,00,61,00,6d,00,65,00,73,00,5c,00,46,00,72,00,65,00,65,00,53,00,\
< 70,00,61,00,63,00,65,00,32,00,00,00
< "MRUList"="a"
<
657c649
< [Software\\Wine\\Fonts] 1392808490
---
> [Software\\Wine\\Fonts] 1392808398
661c653
< [Software\\Wine\\Fonts\\External Fonts] 1392808491
---
> [Software\\Wine\\Fonts\\External Fonts] 1392808398
$ diff userdef.reg*
$