Some messages do not have the timestamp prefix. Many debug messages have the same time stamp, so adding the milliseconds value would be helpful.
Request a feature addition, although I think the timestamp is added by Glib, so we might not be able to control it.
And here is one Enrico prepared beforehand https://github.com/geany/geany/pull/2659
(I have been watching too many cooking shows I think :-)
Cheers Lex