In Notepad++ if the "Mark All" function is used the strings will be colored instead of using a blue point as marker. The advantage is that the string can be easier found in the line and that more occurrences in a line are marked. Notepad++ has even a function that selecting of a word marks all occurrences temporary in another color until the word isn't selected anymore. Both features would be very usefull in SciTE.
You can already do that with "find.mark" as that's described within documentation (http://www.scintilla.org/SciTEDoc.html)
To define the color (yellow in this example), you have to set "find.mark=#FFFF00" into your option file.
For highlight all occurrences of word, issue treats this features :
https://sourceforge.net/tracker/index.php?func=detail&aid=3291636&group_id=2439&atid=352439
I have tested this and found another suggestion. The color of the matches is reverted if the file is changed. I can't find an option for this so maybe there can be such an option added that controls to delete or keep the colored markings after a file change.