I finally managed to figure it out. It's a combination of display cable, display adapter, display in/out, dedicated GPU installed, and UEFI that can cause this issue.
So what I have been using/the setup that makes this issue occur, is a standard low end/scrap pile/workstation grade monitor that only has a single VGA display port on it, a VGA cable (male to male), a display adapter which is DisplayPort male to VGA female, and of course, last but not least, the graphics card which is a GTX 1060 6GB by MSI, which has an HDMI port, three DisplayPorts, and a DVI port.
I noticed that the/this issue only occurs when using:
1. single drive triple UEFI booting with the GPU in
The issue does not occur when using:
1. single drive triple UEFI booting without the GPU in
2. single drive triple legacy booting with the GPU in
3. single drive triple legacy booting without the GPU in
The solution/alternative:
I did a lot of testing, and I found a way to cease this issue at the hardware level by doing something as simple as swapping out the display cable from [VGA to VGA], to [DVI to DVI], and swapping the VGA monitor out for a monitor that has a DVI display port.
-So from this, it seems like it's normal for this issue to happen/occur when using certain display adapters, display cables, and monitors.
From further testing, I found out that I didn't even have to reinstall the operating systems to get the issue to appear and disappear. Simply swapping the display material: [the cable, adapter, and monitor | the cable, the monitor] back and forth, was all that was needed to make the off center boot logo/graphic appear and disappear.
Edit: From even further testing I found out that this issue doesn't occur just for my Z87-WS, but my P9D WS as well. Meaning, it's not just one motherboard in particular that's having this issue, it's multiple motherboards. I can rest a lot easier knowing this. It appears to be a normal/"common" issue. I'm kind of shocked I haven't been referred to a more direct well known fix for this, or something like that.
I was able to find out if the issue occurs for my P9D WS motherboard by installing UEFI OS X/macOS to the OS drive, then partitioning for Windows, then installing UEFI Windows to the OS drive - the partition set aside for Windows, then once Windows was finished installing to the partition set aside for the Windows OS, I used the UniBeast UEFI installer USB to boot to Windows, and the issue occurred doing so. I used this method as a work around, since my P9D WS can't UEFI boot from OS drives for some reason. Either way, it's the same result.