Ponder on or off will usually depend on the tester's hardware. With 2 comps or dual core, I assume all testers would prefer to test single cpu engines with ponder=on, against each other. They may of course still test with ponder=off if they submit results to a tester group which has this condition.
Books and -learning are a kind of philosophy question, IOW what is the normal situation in practise, for which the test result should provide information? Like, you won't test a sports car offroad and you won't test a Jeep in a racing oval. If it is top-level engine sport like the Freestyle tournaments or computer ratings competition, it makes sense to test with individual books per engine with best tuning and book learning.
But that is a very small sector of computerchess practise. For the normal chess player, it's not important in which opening an engine performs best, because for him his own repertoire and/or the opening he explores etc. are important, not what the engine "likes." The engine has to support him in the openings HE likes. That's why for example I use a neutral medium-deep test book (Xmas2640) for the Blivorix tests, which was designed to provide a better variety (wide repertoire). This is much unlike the usual engine books or simple game-based books, where i.e. the Sicilian and Ruy Lopez get a much too big share of all openings played.
http://members.aon.at/computerschach/li ... #downloads
There are two versions, for Fritz and for Arena. It mainly is a test book, NOT a performance book. Some openings which are rare in GM practise, like KG. or Philidor, are not included.
As for position learning and for tablebases, I have set both to on basically, with the exception that I don't use a full 3/4/5-piece tbs. set but a smaller subset.
Only if I use test suites (positions), I delete the learn files before, to ensure "clean" test conditions. Because often, some engines will have analysed in some of the positions before and may have stored something. One could also temporarily move the learn files to another directory instead of deleting them, to keep the learning data.