It's always been my understanding that, by default, the 'Page x of y' and the book title header (if switched on, used to be kepub only but now both kepub, epub) use the same font you have set to read the book.
It's such a long time since I ran using Kobi defaults that I can't confirm this at the moment.
Using patching you can force the 'Page x of y' to always use a fixed font. This will help you with getting Miniclock aligned.
There used to be an option to do exactly this in the standard nickel.yaml patch 'Custom reading footer style'. For some reason it went AWOL during the transition to kobopatch, but you can add it back yourself.
This is the patch code I use. Append it to the bottom of your current patch. I've left in GeoffR's original comments.
Code:
# Uncomment the replace_string line below to use a fixed replacement caption
# font family, for all devices: You can change Georgia to another font name of
# your choice, but Avenir or Georgia are recommended because other fonts might
# not be loaded when the book is first opened and so might cause problems.
# Unlike other strings it is OK if this replacement string is a bit longer or
# shorter than the original.
#
- ReplaceString:
Offset: 514
Find: "#caption[qApp_localeName=\"ja_JP\"] {font-family:Sans-SerifJP,sans-serif;font-style:normal}\n"
Replace: "#caption {font-family:Avenir;}\n\0"
N.B:
- The \0 at the end of the code is necessary.
- Also note the 2-char indent on all of the above code.
- As GeoffR's notes imply, I don't know how well it works if you use a sideloaded font rather than Georgia or Avenir.