Well, the easy solution would be to cut the trim shorter in the room with higher flooring, but I am guessing you are asking because the trim on the tile is already present. What is the junction like between the two rooms? Are you going through a doorway? or does the flooring just change from tile to wood? If there is something like the casing of the doorway to breakup the transition from one floor to the other, I would just put down the trim like normal, nobody would notice the difference from one side to the other. If you aren't that lucky you have a couple of options:
1: You might be able to get away with lineing up the top of the trim and covering up the gap at the bottom with some quarter round.
2: You may also be able to glue a piece of filler material to the bottom of the trim (assuming it is going to be painted). Just make sure the front face of the trim and filler are flush, if you did a good job, the seem will be invisible after the paint.
3: Install some decorative molding on the wall, this serves two purposes, first it provides a good method of defining where 1 area ends and the other begins, and second, it breaks up the transition so that you don't see the height difference.
4: Custom trim ($$$)
5: Redo the trim in the tile area (Atleast the part that is continuous with the transition)
6: Taper the tile trim down to the new trim. This will only work if the taper is very long.
7: All else fails and it just has to be "done"... hide it behind furniture (yuck... can hear my father in the background: "if a jobs worth doing...")

Thats the best I can come up with off the top of my head.

 

You are the only one who knows of the problem with the baseboard height. I can just about guarantee you that if you put the baseboards on above both floors and had a blindingly obvious difference in baseboard height at the change in flooring, no one else would even notice it.

I have the same problem with shoe molding when I install carpet in a living room. The carpet requires the shoe molding to be a little higher than the rest of the floor. Most installers solve that problem by leaving the shoe molding off. It's my building, and I want it on, so I put it on the simplest way I can, with it simply higher than that on the Vinyl Composition tile floor a few inches away.

In 21 suites in 20 years of doing that, not a single tenant has ever commented on that, and I expect the biggest hunk of them never even noticed it during their tenancy.

You might think it looks bad to have the baseboard at a different height and you're going to think everyone else is gonna notice that too. Truth is that 99 percent of the people that walk through your house will never even notice. And the 1 percent that do are going to realize that there's not too many other better ways to do it.