The PHP Encoder trial is available for Windows, Linux, FreeBSD and macOS, and includes a graphical userinterface (GUI) for Windows and macOS, as well as a command-line encoder. This allows you to encode your PHP filesmanually or automate the process with scripting.
As far as using reflection, it's not that hard to disable reflection for an internal function/class (which is what they would do). This wouldn't necessarily error, but it could return garbage. Since the encoders have access to C, assume they can do anything they want.
That's exactly what the encoder does anyway. Except for the public code (designed to be interacted with or extended by developers), the rest is just pointers. All naming information is lost. So obfuscating it yourself isn't necessary.
Are you concerned about someone using your code unlicensed? If so, no encoder can protect you. Because all the user needs to do is dump the opcodes and they can have the code (without variable names, but they don't need that to run it). It's not as trivial as that, but it's 100% doable. 2b1af7f3a8