Ok, we found the issue and I have a band-aid fix for it, should anyone else encounter it and need/want to resolve it for themselves. Though if someone finds a better way to do this, by all means post it.
Since I won't know what hardware ID / registry keys / etc (see my above post) you'll have, I'll use dummy ones, and you'll have to do your best to substitute with your relevant information. Disclaimer: I assume no responsibility for anything that you do with regards to these instructions. You do so at your OWN RISK. Before doing anything, please create a restore point
First, if you haven't already, determine the hardware ID of the device(s) you want to remove from the "Safely Remove Hardware" area. To do this, search for "devmgmt.msc" in the search box of the Start Menu. Find your device, right-click and choose "Properties". In the next window, choose the "Details" tab and then choose "Hardware Ids" from the drop down box. Make note of all of the values that appear. In my example, we'll use "PCI\dummyValue" You can safely close out of everything.
Next, search for "regedit" in the search box of the Start Menu. Right-click and choose "Run as Administrator". (This part of the step may be unnecessary but I am not sure). When the registry editor appears please make a back up of your registry
by selecting "File...Export". Make sure that the export all tick box is selected, and save the file anywhere of your choosing.
Once your back up is made, stay in the registry editor and go to the following key, substituting the dummy value with the hardware id of your particular device.
**Note, in my example I would choose the PCI sub key, but your device may be located somewhere else, like USB
There may be several listings that look similar for your device's id. Look for the one with an option to expand and do so. See my example below:
Next, click on that key, and in the pane on the right you will find a list of different keys and values. We're looking at the "Capabilities" DWORD value.
The last digit of the hex value is what sets whether or not Windows sees the device as a device that should be removed safely or not. If it should be removed safely, then it will likely be a 4. Or 14, or 24 etc (the last digit is 4). To remove that flag, simply set the last digit to 0.
To do this, will require a little bit of fancy footwork. We need to take ownership of the key first. To do so, back in the left pane, right-click on the currently selected key (should be 4&something) and choose "Permissions". Then click Advanced.
Select the Owner tab and select your user name. Tick the box to take ownership of everything in the key and below, then click ok. At this point it may give you an error message or warning, but you should still be the owner. Back at the main permissions screen, check the box for full control, hit apply, and then ok.
Now, finally, double-click on the Capabilities value and in the value box that opens, input your new value. If it is just a 4, then change it to a 0. If it is any other number with the last digit of 4, then change it to the same number but with the last digit of 0. (e.g. 24 becomes 20).
Everything is fixed for now, but if you reboot/logout/shutdown, it will revert. How do we fix this? Here comes that band-aid. Before you close out of regedit, right-click again on the 4&something key in the left pane and choose export. Save the file (just the key, not all) somewhere where you can easily find it. Now you can close regedit. In my example, I called it branch1.reg. Note:
If you have more than one device you want to remove, you will need to do the above for each device. Then follow the multiple device instructions below.
Open Notepad and type the following
regedit.exe /s "full path to .reg file"
You'll replace "full path to .reg file" with the path to that file. I saved branch1.reg to my C:\ drive, so my file would read
regedit.exe /s C:\branch1.reg
*If your path does not have any spaces in it at all, you can drop the quotes, otherwise you'll need to leave them there.
Next save your file as "whatever_name_you_would_like.bat", making sure that All types is selected from the drop down box. Save this in your startup folder: C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Startup
You're all set! The @echo off line will make this silent (you will not see a command prompt) and the /s switch for regedit.exe will bypass the prompt for it to add the information to the registry. Multiple device instructions:
You will need to merge each .reg file into one .reg file using Notepad. Simply open them in Notepad, copying each file's contents into one master .reg file. Then follow the instructions from where you left off above.