Conclusion

As a result of Tilsit, Russia left an entire fleet in the Mediterranean without bases. The two possible routes home had become quiet dangerous. The Turks were unlikely, even during the period of armistice that followed Tilsit, to allow the Baltic fleet into the Black Sea; and Seniavin did not attempt to pursue that route. The chances of returning successfully through the English Channel and the North Sea were rather slight, due to English hostility. The only alternative was to seek neutral ports and to hope for the best. The army in Dalmatia and on Corfu was evacuated through Trieste and Austrian territory to Russia. Some of the ships remained in that port to be scuttled, surrendered to France, or sold to Austria in 1809-10, but, most of Seniavin’s command set sail for the Atlantic, successfully making Lisbon before being blocked by the British fleet and eventually captured. In 1813, two haggard refugee ships, all that remained of one of Russia’s finest fleets, sailed home to the Baltic. Thus one result of the Treaty of Tilsit which is usually overlooked was one of the Russia’s worst naval disasters, a sorry conclusion to a generally successful military performance in the Mediterranean.

p. 222
Russia and the Mediterranean, 1797-1807, Saul (1970)

The history of the Russian Med fleet is pretty interesting and generally not accounted for; just as in the your example of Portuguese history where the presence of the Russian fleet, one of Russia's finest, being at dock in Lisbon has either been forgotten or never generally known. But, it was known to the Royal Navy -spotted first by Sir Sidney Smith - who certainly knew his Russian Ships- and it was Smith who made the first decision to blockade the port of Lisbon for a single specific reason: presence of Russian fleet. He decision -to disobey his orders- was entirely approved as the proper thing to do.

There were certainly other reasons for the British fleet to be off the Tagus, but, the only reason that Sir Sidney Smith was there was to blockade the Russian fleet.