I would hope the regs such as this would be lifted as a common sense reaction to the pandemic: that said we are talking about Gov’t bureaucracy…
My info is dated, but I do not remember boats going to Gib for VAT reasons. We went to Smir after a winter in Barcelona when Gib would have been closer, but I do not remember my thinking from back then. I do remember boats going to Gib for Schengen reasons and the crew having a very difficult time getting their passports stamped and other paperwork concerns to document their stay. But those are random vague-ish memories.
An option that the Canada Border Control allows: going into international waters (12nm from CA shores) and documenting doing so through GPS pics etc. and then returning to check in to a country. This is coordinated with the Border Control officials. That said, even if you were to do so with one country, it may not be honored by the next country you get to: I experienced some officials as salivating at the thought of contributing to their country’s coffers.
If you are on the hard or not commissioned, you might explore putting the boat in “bond” (all countries differ in this terminology) where VAT and other rules might be suspended for the bonding period.
My experience is that attempts to work with the system in good faith, sometimes carries the day as many officials do not generally want to give cruisers a hard time and they might appreciate being given an argument to cut a boat some slack. By that I mean documenting good faith efforts to get your vessel out of the EU (in the ship’s log for ex.). Document calls/comm with Smir or Tunisia and take screen shots of their on-line announcements of being closed. Apply for extensions in the countries where appropriate.
Random thoughts. Please post your further research in this area: you are not alone.
Good luck. My best, Dick Stevenson, s/v Alchemy