Chayei Adam brings down (155:14) that technically yes, one could take a handwritten Megillas Esther, add in the vowels and cantillation marks, and it would still be kosher:
ואין לעשות בה נקודות או לכתוב בה הטעמים מ"מ בדיעבד כשר ואפי' לכתחלה מותר אם אין שם מי שיודע לקרות כהוגן או להקרות לש"ץ
I've heard that some shuls in Israel that want to use a handwritten parchment of the various books of the Prophets for weekly haftarahs use one with vowels and other marks added in, so the reader doesn't need to memorize those in advance.
I understand how you could take the basic text and add symbols, which are not-text. But how do you mark it to note that a word is pronounced differently? Or not pronounced at all, or pronounced despite being not appearing in writing? Can they add notes in the margins? Some other option? Or is there no way to do this?