Is it allowed to use custom barcode mobile apps as a boarding pass?

I think your question is flawed because what is important is the content of the barcode itself rather than how that barcode is rendered on your device. In fact, the TSA (in the US) or person at the gate never sees the application when I place my phone face down on the scanner - all they see is if the barcode contains data that correlates with their internal systems and hence enables you to pass through that particular checkpoint.

In my case the barcode is rendered via Apple's Wallet application, so it is neither the airlines original PDF of the barcode nor the airlines application.

I'm not sure that this is done in the barcode age, but there used to be a website that allowed you to generate fake paper boarding passes that would get you past the TSA checkpoints. Of course, I don't expect that they would get you on a plane, but I think that the idea was to avoid being tracked by the TSA or some such.

The general rule is that if the airport allows for e-Tickets or mobile boarding passes it's fine. If not, and only paper boarding passes are, scanning the barcode and using your phone can cause some trouble.

If the airport and airline are using BCBP (Bar Coded Boarding Pass) then you can modify the boarding pass as much as you want, if you keep the barcode data intact. You can switch from a paper boarding pass with a PDF417 barcode to a phone app with a Data Matrix if you want.

If the airport only uses paper boarding passes then you most likely can't modify the boarding pass at all and you have to use the boarding pass made for you.

If you're unsure if the paper copy is needed - keep it¨(especially if flying with a low cost carrier like Wizz Air). Also, if you're able to have your boarding pass in your phone, don't worry about battery level - once past security you should be able to board the plane using just your passport, or in some cases your ID/drivers license.

This is from my experience and there could be exceptions.

The significance of the barcode lies in the encoded data. If you create a copy of the barcode, it will encode the same data, so it should be acceptable. If you create your own barcode, you will not know what data to encode in it, so it will not be acceptable.

As a general rule, for any company, I would say no! You can't just bring the barcode in any situation. There are several companies that explicitly don't allow this.

Although in theory fine - as others have mentioned - the content in the barcode is the relevant data, you shouldn't use another app unless you're absolutely sure the company accepts it. A notable case is Ryanair. They will only accept your e-ticket if in their own app. This can happen for several reasons:

Commercial reasons Making sure you use their app gives them the chance to cross-sell or upsell stuff to you. Having their app installed is always an advantage to any company

Operational reasons Although the content of your ticket is in the barcode having the ticket with the relevant information printed can still be important. In the case of system failure, they can still look at your data. In some situations, it's faster (and cheaper) to do a visual inspection in an e-ticket rather than reading the bar-code.