Can I drop the “Lond.” in “Philos. Trans. R. Soc. Lond.”?
I wrote to the Royal Society out of curiosity, and received a very helpful answer, along with the permission to post quotes from it here.
So here is part 1, referring to Background in the question:

The answer to the first part of your question is easy. The “Lond” or “London” was dropped from the journal titles a long time ago. Although the Society’s official, legal title is “The Royal Society of London for the Improvement of Natural Knowledge” we now call ourselves just “The Royal Society” and the journal titles reflect this.

And here is part 2, referring to the Question:

As to the abbreviations, there is a huge variety of these and no single standard has been adopted across all publishers for any journal abbreviation system. For example, &quot;Royal&quot; can be shortened to either R. or Roy.
[...]
Our preferred abbreviations are stated on our journal websites, for example.

And I was even provided with some additional hints:

Most science publishers use the National Library of Medicine (formerly Index Medicus) system. Some use ISO4.
Fortunately it no longer matters very much which abbreviation people use, as citations now use the DOI (which carries all the relevant information).

To complete this answer, I looked up the record entry of Philos Trans R Soc Lond B Biol Sci in the National Library of Medicine Catalog. The record entry lists 18 alterntive names/abbreviations for the journal, and contains a note explicating when in the past some of the alternative names were in use.
Lastly, some relevant information could be found in the Fact Sheet:
Construction of the National Library of Medicine Title Abbreviations:

If a journal title undergoes minor changes that do not require a new bibliographic record, the existing title abbreviation continues to be used.
Once the title abbreviation has been assigned, NLM and the ISSN Centre do not go back and change a title abbreviation qualified by place name, even if the place of publication changes over time.

So the conclusion is: someone who decides to use the National Library of Medcine Title Abbreviations consistently will abbreviate

Philosophical Transactions of the Royal Society B: Biological Sciences

to

Philos Trans R Soc Lond B Biol Sci

with a Lond reappearing from its misty past.