The strongest characteristics of the filter's sound are the discreet steps, the clicks and crunches when the frequency is switched, and the phasing effect heard when filtered signals are mixed with the unfiltered originals. The most reasonable assumption is that signals were routed to the filter via one of the four output groups which is corroborated by this account from Bunny Lee:

an’ Tubby’s studio did ‘ave a ting weh you could a thin it, an’ do all different kinda ting with it, right, - it’s not even really equalization, the ting ‘ave four push-up ting, when you push the one in the middle and ‘ave it up and down, with the ting, it create some mad sound, like you hear all some knife a cut thru’.

The 'ting […] in the middle' refers to one of the four bus faders and supports the
idea that it was used as the filter send. Sending the whole mix through the high-pass
filter would not result in audible phasing of the signal, but by sending the signal via a bus it would be possible to mix the filtered sound with the dry sound and this would
make the phase differences around the cut-off frequency audible. This effect explains
the occasional references to Tubby using a phaser.