I know Blender and Fusion, and they both have options to save groups that can be imported into new projects. I think Nuke and Natron(OSS alternative to Nuke) can too.
I cannot answer that directly, normally Zdepth AA is handled by the renderer. For combing different Depth channels you can try the Nuke Non commercial versiom
Nuke and Fusion are direct competitors...so they will have a very similar feature set. Also similar workflow. Z Depth with anti aliasing is handled by the render app actually. Compositing apps just work with 2d images. Deep EXR images will be multi channel and floating point.
What Nuke has with Deep compositing is being able to rearrange layers without holdout passes because everything gets rendered...literally. This introduces new tricks with volume masks and depth slicing. But thomas is right...either you choose a layered solution or node solution. No holy grail and both have caveats.
Blender Z combine node has an "Anti-Alias Z" checkbox (on by default) in its 2d compositing mode. It makes resulting mask for color channels antialiased . Very handy feature texture wise especially for small, few pixels details, hairs etc. I wasn't able to recreate same behavior in Fusion. Wonder if Nuke has a workaround…
Does Nuke differ a lot from Fusion? Curious if it's able to make anti-alised mask when combining depth ? ( like a check box in Blender Z combine node) For some uncertain reason video composers don't find it necessary while for textures it's imo a key thing. In Photoshop at least you could set some blur in fixed pixel…