You can change the icon manually by using a resource editor, such as Resource Hacker.
The drawback of this approach is that the icon will be restored upon the next update.

Currently, I don't plan to introduce an option to choose the tray icon color, but let's keep this topic open and see whether there's more feedback about it.

I'm going to try your win7appid suggestion :D

I think that's the best solution for you. Try it and let me know whether it worked.

You can access the Advanced Options from the main window context menu.

Done in 7+ Taskbar Twekaer v4.5.6.

Should be fixed in 7+ Taskbar Twekaer v4.5.6.

7+ Taskbar Twekaer v4.5.6 was just released. It should fix the issue.

It already works.
If there's a specific option which doesn't work for you, please be more specific.
If you're using an alternative implementation, e.g. UltraMon or DisplayFusion, the tweaker won't work for it.

One way is enabling the "Decombine on..." options. This way, when you e.g. move your mouse pointer towards the taskbar item, it will expand, and will allow you to reorder/detach items.
Another way is using Taskbar Inspector, but that's less appealing.

Old versions can be found here:
https://www.dropbox.com/sh/mcbychsh0xc1dvu/8-Lj2sg3NP

But from your last screenshot, I don't understand what you're trying to achieve. You cannot drag within a combined group with the "Drag within/between groups using right mouse button" option. This option works only with the taskbar items, not with thumbnails.

To reorder thumbnails, you can use the "Thumbnails -> Drag to reorder" option, which is turned on on your screenshot. but you cannot use this option to detach an item from the group.