Your response is correct prior to the royal emigration; however, afterwards, there was no longer any Portuguese fleet left in Lisbon to blockade, so, any designs by N for that fleet were now completely foiled, yet again, by Sir Sidney Smith. The other reasons you state for the blockade are also all gone after the evacuation.
There is simply no question that the only reason that Smith returned to blockade the Tagus was due to the Russian fleet being in that port. Smith was in fact in violation of his orders in doing so.
Certainly, Cook was also ordered to continue the blockade; however, if this had anything to do with factors other than the Russian fleet, I do not know.