I wrote somewhat of a basic crib sheet on this, of which pages two and three directly relate to your question re: ‘the hole’
In short, ‘the hole’ is necessary to provide a flat combined response. Set them too far apart you get a dip in combined response, set them too close and you get a bump. The app presets are a good starting point, because we cannot take into account the room for this, obviously.
In regards to what you should set in your system, I’d bump the preset frequencies up maybe 10-15Hz as a starting point. KC62 is flat well above where you would be sitting a crossover anyway (and FYI, the crossover dial on KC62 is a 4th order (-24dB/octave) Linkwitz-Riley filter. I’d probably start with a 2nd order BW filter for the HPF on your Lyngdorf if that’s an option. Just beware that you should only set a LPF once to the sub - either disable it on the Lyngdorf (if possible) and set KC62 to manual, or use the Lyngdorf LPF and set KC62 to LFE.m
Key thing you’re listening for is no obvious holes in the bass. Room acoustics and speaker/listening position can affect this.
I mean bump up the crossover frequencies of the presets up by 10-15Hz (so start from around 55 and 90Hz) as the LS50 Metas do not have the same bass extension as the actives (due to DSP etc). Only touch gain/dB to volume match the speakers and sub (this will need measurements and/or listening on your part).
Whether you go the manual or LFE setting route on KC62 is totally up to you, just don’t use two LPFs.
And yes, you can still use the stereo inputs when in LFE - LFE mode on our subs simply bypasses the onboard crossover.
This article on Wikipedia helps to explain why Linkwitz-Riley filters need to have the high-pass and low-pass filter 3 db points separated. In a nutshell, it is because they need to be aligned at the -6dB points.
I just got the KC62 subwoofer with KW1 transmitter to add to my original KEF ls50w pair (not the ls50w II). Despite all efforts and all attempted help by KEF support, I have never got the original Connect app to work with the speaker, and at this point, never expect to. Since I have been using Roon, for the most part successfully, with the KEF ls50w, not having that app functionality has kind of been a non-issue. But now with the KC62 subwoofer, that has eliminated the LTE option on the subwoofer, so I went ahead and set up the subwoofer on manual, using the starting point suggested in your crossover “crib sheet”, i.e., low pass @ 45, high pass @ 70, and volume at 3 pm. You mentioned a number of times in the “crib sheet” to be sure if using manual switch on the subwoofer (as opposed to LTE), not to erroneously employ any additional filters in the chain. So I just was looking for confirmation (or not) that my KEF ls50w would not automatically be adding an unwanted high or low pass filter, as again, I’ve never made any prior speaker settings from the KEF app for that speake,r as I’ve never been able to get the app to work.