Can bushes ,tall grass, and flowers use the next combo over?

You can use secret flags to have different undersides if that's what you're saying.

but this is a relatively new feature , so I think they should use the next one over.

No, I think it's fine, myself..

Not all the new things HAVE to make it use the next combo..it would get annoying sometimes. Like if you had multiple bush tiles, but they all used the same undercombo. You would need lots of the same tile. Waste of combospace. A good example is plith's Descendant set..

So, IMO it's fine how it is..

There was supposed to be a rule to do this a while ago. Never got implemented though. I would like that very much, because for some very strange reason, the trick where you put a secret combo on a bush to change the undercombo isn't working for me - it continues to use the screen undercombo (and yes, I've checked and rechecked and it is set up properly). Plus it would allow for multiple undercombos on a screen where there is some sort of secret to trigger.

edit:
Another benefit of this would be the ability to make stuff that you have to slash multiple times (like you can do right now with pound combos), such as a bush that gets pruned away with each slice until enough foliage is gone that you can pass. It would also have uses for custom bosses methinks.