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Now I know this is nothing new to most of you. For the others, here's a couple of photos to illustrate how bad the ports match up on a stock WBX DJ engine.
Didn't quite realise myself until I checked recently.

bit pants!

You want a little miss match for anti reversion, but not that much.

It's even worse with the smaller 1.9 runners.

A tiny anti-reversion step from runner end to gasket won't hurt, but as it is the intakes need to be enlarged a bit just to be as large as the gasket openings, if you don't there is a step-down at just about the worst place it could be.

I port-match every set exactly to the heads they go on. It's easy to do, but beware of the steel shards a carbide burr makes flaring out the runner end castings, they're frighteningly sharp. Wear gloves and an apron, and keep your dogs out of the shop or you'll be picking painful microscopic steel splinters out of their paws.

The manifold is smaller than the port.
The step is in the proper direction.
The only issue I see is the spacer//gasket is larger than either.
If it was a T1 style metal gasket (very thin) it would be NBD.

I would not sweat it.
It will probably still not make a measurable HP difference in any case, and the turbulence may aid mixing.
Only testing would tell if it helps or hinders.

I could see a very tiny step, well under 1mm, might be productive in a carbureted engine ("might", given that creating turbulence in the boundary layer to limit wetting out, although accepted as conventional wisdom, is still quite open to debate). The step here is big, more like 2mm or more, and irregular. I can't see a step there as being anything but detrimental in a port-injected engine, where the turbulent zone below this step is almost entirely above the level where the injection cone of atomised fuel droplets meets the port walls, so all it's doing is lowering average pressure within the port, which means lower mass of air inducted. With port-injection, I'm for having as laminar a flow all the way down the port as possible, I can see no benefit to creating any turbulence whatsoever within the entire air tract from plenum to valve curtain. People can argue the possible benefit in carbed engines, I couldn't care less, but for port injection, it's all the velocity you can get and a step takes away from that.

I totally agree for with your reasoning, but as the air takes a hard ~90 degree turn at the transition with the factory manifolds, it's going to be fugly, regardless.

I half suspect that's part of why WBX run as well as they do. Very effective A/F mixing/quality.