I don’t understand the question - do you have some sort of Render Elements set up, that show only particular objects? If so, what kind, and what is the intention of using them? The Beauty pass should have everything in it, and you could just save that. If you do have Render Elements set up, Save All will save them all to something like an EXR, or to separate images for things like PNG and JPG, so then you should still end up with the result 3 that you can see in the frame buffer.
(if you are just using Render Selected, this would be sequential, doing each render separately one at a time - in which case, I don’t know how you could end up with image 3 in the frame buffer as the VFB can’t add individual renders done at different times)
That is not entirely true if you deactivate “Clear VFB between renders”. In that case if you render 1) and then 2) you get 3). So much for the VFB. If you then save from the VFB you get 3) in beauty but the alpha does not match (it’s the one from the last object(s) rendered).
If you do production rendering, you get the “correct” result: beauty and alpha from the selected object only. IIRC I reported this quite a time ago as inconsistency (the save from VFB is incorrect in this case because alpha and other elements do not match, not meaning the difference between production rendering output and VFB save output).
Using the “Save” button from the VFB should save your image with the mentioned restrictions. But honestly - this is not a workflow I would rely on.
Yes I am using Render Selected.
And No, you could end up with image 3 in the frame buffer if you untick “Clear VFB between renders” and here is the result
But you said “If you then save from the VFB you get 3) in beauty but the alpha does not match”
No, you will not get “3” when you save, you will get it only in the VFB and correct you will get alpha for the last selected element.
The only way to save the whole image is to save as jpeg and this is the point if there any way to save the whole render in other formats.
I think you are a victim of exactly that wrong alpha in this case. I personally never ever use PNG but quickly checked: you would have to disable “Alpha channel” in the PNG setup, it is wrong anyway and is used for the transparency of the PNG. If you disable alpha when saving from the VFB, the result is a png without alpha but RGB is 3).