Well, I'm not a noob, but I sort of agree with the OP.
The current system was incrementally established over 3 decades, and the end result has many side effects that defy logic, and make little economic sense for either the airlines or the passengers. If you look at a MR as a single standalone transaction, the airline would be better off having that seat empty so they could sell it to another, and the pax would be better off not having to sit for 20 hours in coach on that transoceanic turnaround.
Yes, those of you who replied that if you could get RDM or EQM without flying, folks might use this method to buy benefits worth more than their ticket costs. But that doesn't mean that allowing folks to earn miles w/o flying is the illogical part. The illogical part is selling a product (the seat on those flights) and throwing in a bonus (the miles, or maybe the EQM's/status) that is worth more than the price you put on the product.
But, just as legacy airlines have put themselves in a position where they sell seats below cost in order to compete, they likewise need to match other airlines FF programs. Some airlines have tried "more logical" programs where points accrue not based on miles flown but on total fares paid - a far harder system to "game" for us FT'ers - but none have been very successful.