I have added a plane, attached a .png image to it and placed another plane with a separate .png in front of it. This it to create the effect of one image appearing in front of the other when adjusting the clip threshold of the forward most image. The problem I am encountering is when i have more than one copy of this scenario (whether by duplication or just repeating the same process) any adjustments to the additional copies are ineffective and when I make adjustments to the original, it carries over to all copies. I would simply like to be able to adjust the transparency of the copies individually. I am pleading for help.
From what I understand you just need to use a different material for each plane and adjust the material settings for that plane only.
If you duplicate the plane you will also duplicate the material, so if you want to adjust its material separately (without effecting the original) you need to make the material single user.
Once you click on that number (number of users) it will add a sufix to the material name, this means that the material is now “unique” and you can now adjust the transparency of that material only.
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I have, honest to goodness, tried this and every other thing that has been recommended to me. If I may share a video I made of the issue, maybe it would help. I made this video in UPBGE, but I have recreated the problem in standard Blender, so it isn’t just a UPBGE issue. It’s also worth mentioning that when I made the video, I was importing a .dff file with an addon and the two material slots created this function somehow. I have since recreated the same problem by adding a plane with one texture and adding a second plane with the other texture and I get the same results, I am unable to change the alpha independently. Anyway, here’s the link…
Ok I have managed to reproduce this as in your video in 4.0.
I am not sure what is going on, I found that if I set one copy to back-face culling and the other not I can adjust the clip separately.
It does seem to have weird behavior. It looks like clip factor is global for all materials and the back-face culling is per material. 
The clip factor on back-face and front face does seem to be separate.
I would suggest mixing the principled shader with a transparent shader in the shader editor with a “mix shader” node and animating the factor. That way you can also set to alpha hashed or blend and get a smoother transition if you want.
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Holy cow, that worked. I have been on 2 separate Blender discord channels and one other site and you’re the first person who has been able to help me. I truly can’t thank you enough.
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Well I think you have found a limitation of that clip value. I had not come across this before.
Doing this in the material’s shader nodes is more “standard” practice.
Edit: I take this back
You could even use it to make lots of objects disappear at once with just one setting…Interesting.
The clip factor seems to be “joined” only if you use the same image, (even if you set the image to single user in the shader editor.)
So the clip factor seems to be “bound” to the original Image data not the material.
To say I’m green when it comes to Blender would be an understatement, especially with shaders. But I’m diligently learning. I’ve been beating my head against a wall for like 2 days now trying to get past this and I can’t stress to you how much you’ve helped me. A little more information to store in my learning process.
You are welcome, it was an interesting dilemma. I am not surprised you were “beating your head” as it is …lets say weird.
Eevee is great but as much as I like it, things like transparency, reflections etc are a bit weird.
I’m hoping Eeevee Next will improve on some of its shortcomings. I know with the licensing and all I could never really have a lucrative business in it, but as comfortable as I am with the Blender interface and all, I would much rather build hobby games in UPBGE than to try to learn another interface. At least for now.
I am sure it will but it will still have loads of settings to optionally turn on and off.
That is in the nature of real time renderers (or semi real time like Eevee).
The more accuracy the more resources that are used, so depending on your hardware and the frame rates you need, you will want to use certain features or not.
More things for me to have to learn.