It depends on what kind of sub(s) you are using with the JBL 698, if the sub is good, such as the SVS PB2000, or even the PB1000, it will be better to set them to small. That way you will get smoother integration, and the 698 can be crossed at 80 Hz, allowing their 8 in drivers to produce cleaner sound in the lower mid bass and mid bass.
It is hard to believe Audyssey could integrate the sub with the mains at full range, they claimed that, and that bias people to think it sounds better. If you use REW to see the actual performance, I will bet it won't integrated as good as setting the JBL to small with crossover at 80 Hz, okay may be 70 Hz.
I'll be brutally honest, the way you describe the sound is not much difference that people who said the same about hearing such differences between dacs, preamps and amps even when such difference disappear if they compare without knowing which one they are listening to. It is 90% subjective, and biased to the nth degree, sorry! Theory, and verified time and again by measuring, as not really what's happening. But if you prefer the "sound" that way, then stick with it. Other people may prefer the other way, all good in the end, there is no right or wrong, only more accurate or less accurate.
It sucks not being able to use the app, but there are still things you can do, such as trying the reference curve and the flat curve, using L/R bypass etc. Some people don't like the MRC, that without the app you cannot disable it, but many speakers are not affected, or just affected slightly by it, so if you are getting good results then it is not a big deal for you.
Here's my issue I could use your help with
When I'm running music sources like YouTube or Tidal etc that only put out a PCM signal to upmix not Dolby or Auro or DTS X I need to use LFE+Main to engage the subwoofer because otherwise the bass will not route to the sub with the speakers set to large
I am not sure if I understand your question, but keep in mind that the LFE signal get routed to the subwoofer channel only, regardless of the "large" vs "small" setting for the main speakers. You only get the LFE signal routed to the mains if they are set to "None".
Hard to say, because "potent" is a relative term. If you compare it to a 8 or 10" $500 sub, I would say the Studio 698 are quite potent, but compare that to a $1,000 12 inch sub, may be not and definitely can't compare with any SVS, PSA, Rythmik, HSU kind of 12 inch boxes.
No comment on that, as again it is your subjective impression, if I were there I might say the same, or different than yours.
You can do it but there's no use because when you run Audyssey, it will reset everything based on the data collected by the mic. So no matter what you do, when it's done, it (not Audyssey, but Denon) will still set the 698 to "large" based on the so called F3 (ie. the - 3B point).
So, just run Audyssey, let it does its things, and when it's done you go back to the speaker menu and set the 698 to small and crossover 80 Hz. If you use REW to check, you may find that setting to 60 Hz is fine, may even be better, but if you are going just go by ear, I would say 80 Hz is the best choice, that's what Gene would recommend for sure. Going by ear is really cheating yourself as what you will hear would be 99% biased so how good or bad it is, depends on what you mind has already been biased to, or against.
Just by reading my response now, is going to biased you for sure.
@PENG I know your very familiar with Audyssey any advice you can give me?