Can you distribute an iOS app outside App Store using a single bundle identifier? Is there a way to distribute an iOS application to customers with a single bundle identifier outside App Store?

The software firm I work for is providing iPad software to several large companies. Right now we're using the Apple Developer Enterprise Program.

Each of these companies receive an IPA file with their own bundle id e.g. com.SuperApp.FirstCustomer, com.SuperApp.SecondCustomer. The companies install and manage our software using their own Mobile Device Management (MDM) system.

A 3rd-party component we would like to use in our software, PSPDFKit, is a lot more expensive if each of our customers have a dedicated bundle ID.

We don't want to distribute our software through App Store, we just want to send the IPA files directly to our customers – and our customers also prefer this way of the app distribution.
You should not be using an Enterprise Program membership in this way. The Enterprise Program should only be used to distribute apps to devices owned by the enterprise member company I.e. your company's devices. 

You can use a regular organisational Apple a Developer membership to distribute a B2B to your client organisations. 

You use App Store Connect as for a normal App Store app, but in the pricing and availability section you make it a private app and list the Apple Business Manager organisation IDs that are permitted to access the app. 

As well as being "the right way", B2B apps are lifetime signed like any other App Store app; you don't need to worry about refreshing distribution profiles and signing certificates periodically. 

There is a great WWDC 2019 session that covers this.