It's no secret that "the average guest" turns their brain off when they come to the park; there's a decades-long running joke about guests asking "when is the 3pm parade?" that illustrates this very premise. And if the "average" guest is dumb, statistically you have to assume that about half of the population of the park is even dumber.
It may not be Disney's responsibility to fix that, but it is their responsibility to create a system that those folks can work within.
It's no different than designing a theme park that is able to operate comfortably under weather conditions that can be reasonably anticipated. That's not to say that the parks need be functional during a Category 5 hurricane, but there should be shade from hot summer sun, shelter from storms, adequate drainage for rain, etc. But of course, Disney has struggled to design theme park spaces with those basics recently as well.
Especially because FP+ and LL weren't something that anybody wanted, but rather were forced upon guests from the top-down, these sorts of things need to be taken into consideration. If you're forcing a new system to replace one that was mostly intuitive and works fine, it's your responsibility to make sure the new one is an improvement (or at the very least, a lateral move) over the old. And I'm not sure that the current system is an improvement in any meaningful way, other than to Disney's balance sheet.
While guests may not have PhDs in theme park planning or fully understand the (let's face it, not very user-friendly) digital interface, they're not total morons. They know that something has gone wrong, and that there is a growing line of other guests impatiently breathing down their necks while they block up the path. It is discourteous to leave them there like that, rather than discretely addressing the issue out of the way from the near-constant flow into the queue. It's also discourteous to the other guests queueing up behind them who (presumably) paid extra for the privelage of having to wait for somebody else's unrelated issue to be resolved before they can get on the ride.
I have no idea what the current training protocol is, but if CMs are being told that discretely resolving issues is discourteous, that is a massive management failure of a company that once claimed to be a customer service leader. Yes it ultimately comes down to the tone of the CM addressing the issue, but it's hard to imagine guests getting upset about being asked to step aside while their issues are dealt with; they know they're in a crowded theme park, so it's not unreasonable for them to need to make room for other people as well.
Additionally, these issues pop up constantly at nearly every attraction in all four parks all day long. Having to wait for a specialized guest relations cast memeber to resolve them is ridiculous. The attraction CMs should be trained and empowered to deal with most of the routine issues on the spot. Yes, there are some bigger issues that may require more specialized solutions (particularly anything involving payments), but most of the problems are rather routine and should be able to be resolved quickly and easily. Having to call in CMs from another location wastes the guests time, creates redundant staffing, and ultimately cheapens the whole experience into a cattle call rather than the best-in-class that Disney claims to be.
As for the pysical configuration that's currently being tested, it took a solid 5+ years for them to really figure out how to set up queues to somewhat-efficiently handle FP+. They had to train guests on how to use it ("touch Mickey-to-Mickey"), add and/or rearrange the touchpoints, create pre-touchpoint queue space to keep walkways clear, relocate CM podiums, add mobile iPads, etc. until they settled on a flow that worked for the particular location, space, and capacity. Very few (if any) attractions kept their original configuration with no changes throughout the FP+ era, and there really wasn't a "one size fits all" solution for how to configure the attraction entrances.
And, although they function similarly on a surface level, LL is far more complex in terms of "what could go wrong" with a particular guest's reservation, and Disney's infrastructure (both physical and procedural) needs to be able to handle it. It should have been in place when they rolled out LL more than a year ago. That they still haven't figured out a smooth way to deal with these constant daily issues is nothing more than a basic customer service failure.