This is no different from the previous microcore plus extensions.
Most X extensions did not depend on Xlibs simply because tinycore did not reveal to tce-load that Xlibs was loaded.
Now that there is no tinycore.gz, loading applications work as they always did for microcore.
I always have Xlibs first in onboot.lst when using X.
When I am not using X, I don't try to run X applications.
One of the advantages of the new core approach is that now it will be possible to include Xlibs as a dependency,
where this was not practical with tinycore.
So, unless/until all X program maintainers update the all the X extensions, you will just have to live with it and use your head.