Tosfos Yeshanim DH Misfeika (on 52a) suggests that the reason that a single Peroches on the outside in Bayis Sheni was insufficient according to the Rabanan is because we are concerned that the Kohen Gadol might offer the Ketores in front of the two Badim that protruded through the Peroches and it would turn out that he was not in the Kodesh ha'Kodoshim. But there was no Aron in the Second Beis Ha'Mikdash?
I thought about this many times over the years, and came up with a unique answer.
The Paroches had two "bumps" in it as though the Aron was there on the other side. Either by design or a ness (my svara). As the other ten nissim did continue in the Second Bais, the Schina was there - although at a lower madraiga - for four hundred and twenty years.
On the same subject, Chazal tell us that the Kruvim faced each other during the churban (to show that HKH took out His Chaima on the eitzim v'avanim. But who went into the Kodshai Kdoshim to see it? and there was no Aron there during the churban as the Aron was already hidden, and definitely not by the Second Bayis.
My answer to that is that there were Kruvim knitted into the Paroches, and those Kruvim moved, and that was what the ness that people saw.
Maier Solomon
This is a very interesting idea. I am just going to make a couple of very brief comments for the moment but this certainly deserves a lot of further thought.
1) Firstly I am not sure whether we can make up new miracles on our own. I know that the Gemara above, end 21a, states that the 10 nissim mentioned in the Mishnah in Pirkei Avos only refer to miracles which happened outside and were recognisable to everyone, whilst nissim which happened inside; and which not everyone saw; are not related in the Mishnah. According to this, the ness about the bumps in the Paroches would not have to be in the Mishnah. However, it may be that oniy Chazal have the power to mention new miracles, but we do not.
2) I found that the Siach Yitzchak on the Tosfos Yeshanim that you cited (which is pirnted on 51b DH Mesafka in the older editions of the Gemara) asks your question. He answers that even though there was no Aron in the second Beis Hamikdash, nevertheless the Cohen Gadol might behave as if there was, and mistakenly burn the ketores in front of the two Badim. It seems to me that there is not so much difference between your answer, Maier, and the answer of the Siach Yitzchak. Both answers are trying to equate the second Beis Hamikdash to the first one. Siach Yitzchak writes that this may happen through a mistake, and you write it could happen through design or a ness.
KOL TUV
Dovid Bloom
Comment about Kruvim:
We should not forget that the Gemara Yoma end 54a tells us that there was another kind of Kruvim in the Second Bayis. These were the "Kruvim deTzurasa". Rashi (end 54a) writes that they were painted into the stone walls or engraved in the wooden walls. The Ritva Yoma 54b cites an opinion that these were the Kruvim about which Chazal say that they faced each other during the Churban. This is similar to your answer. Maier.
Behatzlachah Rabah
Dovid Bloom