Sry, i ran out for a bit..
Now, you prolly ment %locked On, %win.ini <1st encryption>, %mirc.ini <2nd encryption> but.. have u actually tried it? :)
As for direct answer, this method is more secure (& better) because:
1) when u lock ur mirc with built-in locker, u can open it on any system without reg changes (ex. ur friends comp or 2nd sys on ur machine);
2) for the same reason, if u lock one instance of mirc, all other will be locked too which is pretty unpleasent if u script or something;
3) due to its nature, build-in locker might have problems under wine. (not tested);
4) u cant remove protection by simply deleting/changing variables from remote.ini (in case u find em 1st), in fact u will make things worse as u wont be able to open it at all until u copy vars back;
Anyway, u gave a good point, if this was separate .mrc file u could simply delete it to break script based protection. Thats why I added detailed instructions of passlock implementation for scripters in \'Author\'s Notes\'.
Thx for input Yoinx. :)