In Rhino 5 SR12 64-bit, indeed layers are reversed in order when moved to Illustrator via either Export or Export Selected.
However, what is here being called “layer order” seems to be merely the obscure order the layers were created instead of the actual Layers palette layer order, since once I rearrange that order, not a thing changes in the Illustrator order. It’s deceptive if you happen to have created a stack of Layers palette layers manually and then think you are exporting that order. No, you are not, the order just happens to match their creation order! This means Illustrator export is broken, not just quirky, since mere reversal is fixed with a single Illustrator Layers palette pop-up menu command, but there’s only manual labor to fix layer order.
Obviously sublayer structure is desired too, but that’s easy to fix manually, by flattening your sublayers in the Rhino Layers palette via selection and using the un-nest left arrow button. Otherwise sublayers obtain long compound names like Layer02::LayerX which isn’t very useful since Illustrator won’t automate layer name and nesting changes well via Actions.