Well, it's true (as far as I know) that you have to override each
properties file separately, but any overrides you do should be done in
your user properties file.  This way you keep them all in one place
and you don't have to redo them if you go to a newer version of SciTE.

I admit it is cumbersome to have a set of overrides for each lexer,
but you only have to do it once.  I haven't made any major changes to
my properties in years, and the only time I have to do it is when I
start using a new language I haven't used before.

Also, if you want to keep the styles more-or-less consistent across
different lexers, use the symbolic names instead of hex codes.  For
example, I've set

# Comment
style.python.1=$(colour.code.comment.line),$(font.comment)
# Number
style.python.2=$(colour.number)
# String
style.python.3=$(colour.string),$(font.monospace)
# Single quoted string
style.python.4=$(style.python.3)
# Keyword
style.python.5=$(colour.keyword)

and so forth.  Similarly, any lexer that I use regularly has its
properties overridden in this manner.  Now I can change the color of
numbers in all the lexers *that I use* by modifying just
$(colour.number), earlier in my user properties file.

I agree that the design could have been more flexible and easier to
customize.  But going back to fix it now would probably be a
tremendous amount of work, and more trouble than it's worth.

John