Many of the benchmarking related formulas are present in the out-of-box version of the Cost Source Master Data table...even for those who are not (and may never) use benchmarking. Presently, we are not and do not plan to use benchmarking. If we decide to deploy benchmarking later, it's an easy enough task for us to revisit and address the errors raised as part of that deployment effort. For now...just noise.
If I was striving for perfection (and had the time to do so), I would eliminate all of the "warnings" so I can better focus on the real errors (deserving of my time).
As it is, it comes down to how us as users of TBM Studio wish to tackle the errors. For me, I choose to consciously ignore many of the error counters/flags since they do no harm to my CT projects now or in the foreseeable future.
For me, my time could be solicited better if Apptio qualifies the flags raised in some way as Informational, Warning, Error, or Critical and provides a means for me to filter on/out based on these qualifiers to those I don't need to worry about (eg Informational), ones to worry about later (eg Warning), and those I should look at now (eg Error and Critical).