[Allsquared]

I am pretty sure the reason this rule exists is at least partially due to the history of the rule change.

When thick sponge rubbers were introduced to table tennis, the vast majority of players didn't like it and wanted to ban them. However, for a rule change to be approved, a 3/4 majority of associations was needed on the ITTF level. Ironically, this 3/4 requirement existed, so that the sport could not be changed fundamentally without vast support, but now the sport was changing fundamentally, and all of a sudden you need to 3/4 majority to keep it from being changed.

Anyway, Japan managed to convince enough associations to have a blocking minority, so sponge was being kept allowed. There was a real threat of a split within ITTF, because all European nations wanted to allow only hardbat play. England even banned sponge rubbers internally without it being banned on ITTF level (one of the reasons England fell behind from being a nation producing world champions to an also-ran).

In the end, what was allowed was a compromise between the sponge party and the hardbat party, but it was formulated in such a way to fool the hardbat party into thinking they had almost won, by saying that only pimpled rubbers are allowed, restricting the thickness, and then saying that a layer of sponge is allowed under the pimples and the pimples may also face inwards.
Remember, at that time the point of controversy was thick sponge rubbers, and they were banned, and the pro-hardbat associations thought now only pimple rubbers would be allowed, and the thin sponge layer underneath wouldn't make that much of a difference.
If the rule was formulated to say that sponge rubbers are allowed, and you can put a layer of rubber on top of the sponge, the pro-hardbat associations probably wouldn't have accepted this "compromise".

At least that is my theory.