(Note: IANARFE)
There is a difference between prioritizing antenna performance over physical design, and maximizing antenna performance. Maximizing antenna performance isn't really necessary if the signal is "good enough", meaning you wouldn't drop calls when you hold the phone, for example. Prioritizing would mean "this adjustment would look nicer, but we would start to drop calls if we did it", and they are suggesting those adjustments would not be made.
Also, I believe the older rod antennas would be for the 900MHz spectrum, rather than the more modern 2.4GHz spectrum. You can fit an entire quarter-wave antenna inside of the case of a cell phone easily now (although of course having an antenna that extends above the head to get a clearer signal would still be beneficial)