This is purely a terminology issue - I'm just requesting that the channel label be renamed to prevent user confusion. No behavior changes are required.
This is important because the "subwoofer" channel and the "LFE" channel are not the same thing, and using the wrong term can (and in fact, has) cause lots of confusion. I'm referring to the SPEAKER_LOW_FREQUENCY channel in the WAVEFORMATEXTENSIBLE structure documentation.
The major difference between the LFE channel and the subwoofer channel is that the former technically only exists before bass management (also called "bass redirection" or "crossover") has taken place, while the latter only exists after that. However, APO processing always takes place before bass management has taken place, as bass management typically occurs in the sound card driver or hardware, or in the connected AV receiver. If the channel is labeled "SUB", the user could be misled into thinking that the channel contains redirected bass from the main channels as well, which is absolutely not the case.
One could argue that Equalizer APO can also be used to do the bass management itself, and this is absolutely true, as the software clearly is flexible enough to do that thanks to its advanced channel routing capabilities (which is amazing, thank you!), but even then, the channel still starts as LFE, only to be "converted" to SUB later in the Equalizer APO filter chain. So, in order to be as general as possible, the best name for the channel is probably LFE.
For more background information about the difference between the subwoofer signal and the LFE signal, please refer to Appendix 1 of the ITU-R BS.775 international standard, which describes this issue in excruciating detail.
I concur with you. The reason the channel is currently named SUB instead of LFE is from the time E-APO did not have a GUI. I wanted to make it easier for the normal user by using the same channel names as are used in the Sound control panel when configuring the channels.
I did not know about the distinction between subwoofer and LFE so it is nice to know. To know that bass redirection can still occur after E-APO is very important (I added an extra warning in the Documentation Wiki for this), so that is another reason to change the name.
I will rename the channel to LFE in a future version but of course keep SUB as a valid name for the channel so that existing configurations continue to work.