Physical co-clustering of two or more logical relations/tables in modern RDBMS
Is co-clustering still a valid option for optimization?


Sure, it is a valid option for optimization, if your DBMS offers it. As David Browne has mentioned in a comment, only Oracle does (which, in a way, tells you how practical this feature is). 

As you have noted, it is useful in a very limited set of scenarios, while being detrimental to a wider range of queries. In the cases that might benefit from table co-clustering you can employ alternative optimization techniques, such as materialized (indexed) views or column-organized tables, which offer similar performance benefits while being more widely available.

Consider also that today common use of SSD storage, abundance of cheap RAM on database servers, in combination with better query optimizers, decrease the value of marginal reduction in physical I/O at the cost of possible negative side effects and additional database maintenance overhead.

TLDR: don't bother.