Total read count of shotgun affected by few highly abundant sequences
That sentence in the Anders and Huber paper is a bit misleadingly worded (I don't think that was their intent). What they mean is that highly expressed and highly differentially expressed genes can out-compete the majority of the other genes, which thereby leads to them appearing to have lower expression if one uses total read counts for normalization (basically, what you said in the second paragraph).

An alternate interpretation of what they wrote (likely the one you understandable understood to have been their meaning) is that some highly expressed genes will inflate the total number of reads a sample actually gets. I have yet to see this in practice, but it certainly COULD happen. There are technical biases in sequencing such that some sequences (often due to length and GC content) are easier to sequence on common machines. A good example of this would be PhiX, which forms clusters much more easily on Illumina machines than real samples. I expect that this is relatively rare in practice, but using a more robust normalization would still help in protecting against it.