The solution in this instance was to override the locations of the cache and logs directories according to the cookbook. This, however, by itself causes the cache:clear
command to fail. The answer to that problem will have to appear in another question if I can't find it on my own.
Update
The other solution here cannot work because any php setting in .htaccess when Apache server is running FastCGI will cause a server error. Clearing the cache was never solved so the site was moved to a non-CGI host.