Well I think the simplest explanation is that the strength of Reaper beams vary greatly depending on the needs of the plot.
The Leviathan's method of control works completely differently than Indoctrination, the Leviathans use straight up mind control where as Indoctrination is more akin to psychological manipulation. I'm not exactly sure how you concluded that Reapers have an improved version of Leviathan mind control, that quote you gave just talked about the Reapers developing Indoctrination (which in most aspects pales in comparison to mind control).
I'm less sure where you are going with the last paragraph. Are you saying the Reapers let Shepard go on purpose? Implying that they could totally stop him at any time? That makes it seem like Shepard just wins because the Reapers are dumb. Like did the Rannoch Reaper not sweep the beam because it was throwing the fight?
If each Reapers possesses the ability to influence organics, and the Reapers have over the ages perfected that to indoctrination, then why should that exclude what Leviathan does? How is altering your sensory input not an ability to influence organics?
Harbinger was made from the essence of the Leviathans. ("From our essence, the first Reaper was created") The essence of the Leviathans is the will and the ability to dominate all.
As for my last paragraph, I wasn't saying the Reapers are letting Shepard go on purpose all the time, no, their efforts to kill Shep are sincere. They perceive Shepard as a threat. But like Leviathan says, they must be aware that Shepard's victories are not merely a product of chance. Shepard is a special kind of determined and strong willed, "Your confidence is singular". But we know from ME2 that Harbinger even wanted Shepard's dead body. So I really think that they do not really care if they take Shepard alive or dead, it's just that Shepard alive is more useful to Harbinger, that's why we're being lured to the beacon. The Reapers simply create a situation where we have no other choice than to make a push for the beam. Then when Harbinger has dealt with most of the resistance, he fires a near miss at Shepard and hacks his sensory input.
In summary, the only moment I believe they let Shepard go on purpose is at the beam run.
EDIT: As for Shepard winning because the Reapers are dumb... no. If the ending is an illusion/simulation/hallucination, then Shepard didn't actually defeat the Reapers. They would succeed turning Shepard in control and synthesis, and in destroy, they'd simply kill Shepard. It's possible that that is why Shepard dies in every possible scenario except when there's an unusually high amount of war assets. (Which seems to suggest there were enough war assets to ensure Shepard survived)