Because if you change the htaccess (which you should to fit your needs) it would get overwritten by the standard htaccess if it would have a leading dot.
By removing the dot in the installation file you are save to overwrite the existing files with the files from the new update.
This actually makes it much more easy to update.
When updating you dont need to change the htaccess (unless the original one changes).
If the original provided by the update changes you should adapt the changes.
If you provide me (via PM) some temporary access to your server I can have a look at it