I made tons of interesting discoveries since last night

I was wrong. It does pay to continue testing. Now I feel like a mad scientist because my messy room is filled with scattered PC parts and their packaging. This will be a long post.
TLDR: Don't put a drive tray or other objects above a 3.5" drive's labeled side because there will be whiny noises.
Let's get over with first the
Bad News:
I broke 2 of my Be Quiet! Silent Wings 3 140mm PWM fan's rubber push pins in a semi-frustrated state after further hours of diagnosing and testing the WD Blue noises

. The remaining 2 pins are intact, but it's now pointless to leave the fan hanging. It's unsettling. I'll try the metal screws later

. It was hell trying to pry them out from the mounting spots on the front of the case, contrary to how simple it was to push them in initially. That coupled with my fatigue and cold I've been experiencing didn't help.
Good news:
I can eliminate the drive's whiny noise! All that's left is the air noise it makes that's the most challenging to kill without a specialized enclosure or DIY solution. The rest of my PC is silent in the dead of the night if I really focus my attention (when idling of course), with occasional fan noise that's super faint that I couldn't identify; it's likely a normal result of all fans combined to the point that sometimes I second guess whether the PC is powered on

.
Discoveries:
The WD Blue's labeled side is where the whiny and air noises emanate. When I place my ear next to all its edges and the other side, from various angles, a huge portion of the noise is blocked off/missing. So why did I first mentioned the noise signature is the same outside the case with my hand holding it vs inside the case, same for the WD Red? For some reason when I cover the noisy side with my hand, or without touching my palm but still close, the drive instantly creates a higher frequency noise. I then tried placing the case's drive tray over it (still outside the case with the other hand holding the underside of the drive) and it made the same noise. If only part of the bottom or top half is covered, it doesn't make the noise. It seems most dominant near the centre area of the drive. Then I tried covering it with a thin dish washing foam over it, but the noise isn't there. Maybe any object of considerable density or weight covering it is causing this annoyance? The Fractal Define C drive cage only holds 2 drive trays; my HDD was on the lower tray and SSD on the upper tray. Switching the HDD to the top tray and without the SSD connected didn't improve the result, but leaving the HDD on the lower tray with SSD on the upper tray both removed from the cage and case did! When the HDD is in the tray and pushed part way into the cage inside the case, the whine isn't there, but when fully inserted it's there. This bolstered my hypothesis that when something of substantial mass (in this case the SSD, drive tray, or both together on top of the HDD) is in proximity of the HDD noisy side, a whine is created. My next step was removing the drive cage: "Curiosity killed the cat", but in my case it killed my fan push pins (see Bad News above). It was getting late and I was exhausted, so my observation wasn't sharp and it could have been placebo, but the HDD sounded slightly quieter without the cage and just simply placed on top of the case floor without any proper mounting. Perhaps it likes even more breathing space above it with no cage or SSD above it, but what to do about that broad sounding air noise it generates if the best position is supposedly with the noisy side facing up? While I've achieved a little victory, the result is about half the sound of my external WD drive. Still not completely satisfied, I wanted it to be more quiet, and that I did achieve if only in my sleep...
This morning, I conducted further experiments. With the HDD's noisy side placed on my carpeted floor, the whine wasn't audible. Why not

My floor is certainly more heavy, massive, and dense than my hand. I've begun to think it's more accurate that this occurs when a nearby object of considerable mass with an
uneven surface is covering it. It's probably because my palm and various objects like the upper tray and case structure have gaps and holes that the air noise seems to resonate negatively and changes its noise characteristics, akin to whistle blowing. Curious, I re-placed the HDD on my carpet and applied pressure by pushing it down -- in addition to the lack of whine, the air and overall noise is greatly muted! This is the quietest state of the running HDD I've heard so far and I would love to transfer this noise level with it placed inside my case! While carpet is apparently an uneven surface, this may not be surprising because the air noise is probably more evenly distributed/bounced/spread across the floor. Then I re-mounted it into the lower tray and cage, but this time upside down with the noisy side on top of the case floor above the ventilated holes. Surprisingly, there was no whine. Maybe because the case floor is so thin and it's a non-massive object?
On to my current status: the HDD is placed on top of my anti-static foam that came with my PSU

. I will report back and hopefully arrive at the best conclusion.