The timing difference is due to the fact that, when you have 3 INS units installed, they, by default, enter Triple Mix operating mode, which is obviously, as the name implies, NOT available if there are less than 3 INS units available.

Triple Mix-ing is considered an aid to INS positioning as DME Update, so the API (Actual Performance Index) "grows" slower.

Try, with the concorde, or any aircraft you have with 3 INS installed, to command MI 5 operations performing "eradication" (see operationsmanual.rtf) by simply entering 1, INSERT while in DSRTK/STS (to disable Triple Mix), and you'll see the API increasing as fast as in a single or dual configuration.

So, to answer your questions, yes, this is normal and no, you can't change this behavior as it reflects the way the real one operates.

> How were the early transoceanic flights crossing with INSs ?

As far as I know all aircraft capable/certified to fly over large water areas were equipped with triple INS. B707, DC-8, Classic 747, DC-10, L1011, Concorde, they all had 3 units installed.

BTW to enter MI5 operations you don't need to perform eradication, you just need to command MI5 by entering 5, INSERT while in DSRTK/STS.
My mistake, sorry. If you need more details then please see OperationsManual.pdf.