Something in your init file is invoking
font-lock-fontify-buffer. You can track it down and see if you want to change it as suggested by the warning. Or you can ignore it.
Emacs has added a ton of byte-compilation warnings in recent years. Most can be ignored, in the sense that there will be no negative effects. Most of the time they serve mainly as suggestions to library writers to update code.
But even in that context many, perhaps most, can and should be ignored. If a library supports older Emacs versions as well as newer ones, and if it handles this cohabitation properly, such warnings will likely result. This is simply because the byte-compiler analysis cannot determine that they in fact do the right thing. Its analysis is pretty primitive, even though it can be helpful by drawing attention to something that a library author might want to check.
And yes, even though you are not explicitly byte-compiling anything when you load your init file, the byte-compiler can kick in and do some work. So you can get byte-compiler warnings without being aware that you are byte-compiling.
To your bottom-line question: You can ignore this particular warning. Nothing bad will come from code that invokes
font-lock-fontify-buffer from Lisp. In some cases the result will not be what the author might have hoped for, but there is no risk for you from such a Lisp invocation.
If you are curious about which part of your init file causes this, you can recursively bisect the file to find the culprit. You can use command
comment-region to comment out a selection of text (and with
C-u to uncomment a selection). Comment out 1/2 of the file, then 3/4, 7/8, etc., to narrow it down to find which part leads to the warning.