That won't enter control characters (0 to 31), just "high" characters (code 128 and above).
Actually, you're falling for a lie by Microsoft
Alt-1, Alt-2, ..., Alt-31 do enter characters that LOOK like the control character signs in the VGA charset. When you save the file, they'll get converted to question marks. If you read the message when saving, you'll see why: these signs aren't actual control characters, but lookalikes from Unicode. They can be loaded back if you save as UTF-8, but DarkPlaces does not support UTF-8 as of now.
This lie is as old as Windows 3.1, though: Alt-digits... enters characters from the DOS code page, and get translated to Windows's charset. To get ACTUAL character codes, you have to prefix the number with a leading zero. E.g. Alt-010 will enter an ACTUAL line feed. However, Notepad doesn't insert these characters literally, but executes their associated commands. E.g. Alt-01 does NOTHING in Notepad, and Alt-08 deletes the last character, instead of entering a literal backspace character.
1. Open Notepad
2. Paste: ÿþMSMSMS
3. Save
4. Open the file in Notepad again
You can vary the number of "MS", so you can clearly see it's MS which is causing it.