Wouldn't that be nice!? It would eliminate all those complaints about clipping not removing the unwanted parts, like true cropping does. And wow! Clipping is a pretty big feature not to support. Hopefully they can get it working soon.
The only way I can think that you can do it, is to use path operations instead of clipping. (mostly Difference, Intersection and/or Cut Path, probably) There is a Multi-Boolean extension which allows you to perform many operations over many paths at a time, instead of only 2 paths at a time. That could help significantly. Let me find that link.....
https://inkscape.org/en/~Moini/%E2%98%85multi-bool-extension-cut-difference-divisionClones could come in handy too.
Have you confirmed that it officially doesn't support clipping? Or did you just surmise it, because of what you observe? After further thought, you might investigate whether it is clipping that isn't supported. Because if you have groups which are clipped, and the Unity plugin didn't support groups, then the forced ungrouping would result in unclipping.
(That little beauty of an aggravation was introduced with 0.91, iirc. Before that, you could ungroup, and everything remained clipped. I don't think it's actually a bug, but it bugs me (haha).)
Hhmm, if it doesn't support clipping, it probably doesn't support masking either. But if it does, you can probably find a way to use masking instead of clipping.
Sorry, I wish I had a better answer for you.