I did it like this (using Kroeger 05_55 pixel font). The version of this font is Bitmap (.fon) and it only has one size (very, very small), so any size that the OS tries to set gets ignored
Windows Registry Editor Version 5.00
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Fonts]
"Segoe UI (TrueType)"=""
"Segoe UI Bold (TrueType)"=""
"Segoe UI Bold Italic (TrueType)"=""
"Segoe UI Italic (TrueType)"=""
"Segoe UI Light (TrueType)"=""
"Segoe UI Semibold (TrueType)"=""
"Segoe UI Symbol (TrueType)"=""
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\FontSubstitutes]
"Segoe UI"="Kroeger 05_55"
"Segoe UI Light"="Kroeger 05_55"
"Segoe UI Semibold"="Kroeger 05_55"
"Segoe UI Symbol"="Kroeger 05_55"