knowj,
There are many projects, code & items I have downloaded in the past that disregard 'best practices' with regards to E_NOTICE.
I personally prefer to follow them, albeit additional coding, it will generally help you with future releases of PHP.
For instance short_tags was quite common for a while and now, due to XML is considered a bad idea.
In the end of it all, if you're planning on releasing the software in any capacity (and especially if you are charging for it) you should follow best practices since you may not be in total control of the server environment, whereby sys admins can block out functions, such as ini_set() and error_reporting(), effectively making your script announce to the world about the undefined indexes.
If this is on your own server (VPS/Dedicated) and you have control over the environment, and that's where the code will be kept, you can really do whatever makes you feel comfortable.
That's my take...