I'm not sure what the default charset of Komodo might have been, but any given text editor will have its own behavior as far as how it encodes text. E.g., if you have some editor (say Notepad or Komodo) and you create a new empty document, paste in some text from god-knows-where, and then save it as myfile.txt, then you might not be able to make any assumptions about what charset is used. It's been my experience on Ubuntu that pretty much all text I create in this way using nano or gedit is UTF-8. On a windows machine using Notepad, it's often been Latin-1. In either Ubuntu/Gedit or Windows/Notepad, you can change the default character encoding using "Save As..." The resulting dialog has a drop-down that lets you specify the char encoding you want. I have no idea if Windows/Notepad will add a Byte-Order Mark (BOM) or not.
On my Ubuntu machine using Gedit, I opened a new empty document, typed a single A character, and saved it as /tmp/foo.txt and I can inspect its contents using the xxd command:
$ xxd /tmp/foo.txt
0000000: 410a A.
This tells me my file length is two bytes, the first being 41 (hex for "A" in both ASCII and UTF-8) and the second being 0a (hex for a line feed in both ASCII and UTF-8). Note that for ASCII chars (basic ASCII, not extended) their encoding is the same single byte as their UTF-8 encoding. There is no BOM in my file.
If I'm a bit more adventurous and replace the A in my file with æ from your example, this changes things:
$ xxd /tmp/foo.txt
0000000: c3a6 0a ...
My file is now 3-bytes long. I'm guessing that æ is encoded with two bytes (c3a6) and that we still terminate the file with a LF char.
Another key issue is that one's PHP files can also be saved with a text editor and encoded as UTF-8 -- or not. It's important to recognize that the PHP language specification only makes use of ASCII chars, but when you create a PHP file, you can save it as UTF-8 and when you type string literals, you can use non-ASCII chars like æ:
// save this file as utf-8
$my_utf8_string = "æ";
If you were to save this file as Latin-1 instead of UTF-8, you might get a different encoding for æ other than c3a6.
So once you get clear on what charset is used for strings that you get INTO your PHP script -- either by reading external files or by defining strings in your PHP file itself, then you can start to concentrate on where you plan to send these strings. Want to show them in a browser? Declare your charset as utf-8 so the browser knows. Want to put them in a database? Make sure your connection to the db uses utf-8 encoding and make sure the db and/or table and/or column you are storing the string in are all declared as utf-8.
Getting charsets right is all about understanding the chain of custody for data and making sure that any required translations happen if charsets change in that custody chain. E.g., you might have to translate from utf8 encoding to latin-1 if your database table has a column that is latin-1 encoded.