With serial configuration, the battery voltage is doubled, so half the current has to be drawn compared to a parallel configuration. Within the parallel configuration, the batteries split the current as well. So it's basically the same result for the batteries, the difference though is that one can't detect via the chip how many batteries are in parallel, so it assumes only one. There's also other factors that favor serial configurations for high power, such as that the more amps you use, the larger conductors and more heat dissipation you need.
For example, while you assume that the battery amp limit is doubled, this is unlikely true, because the conductors to and from the parallel configuration likely can't support 40 Amps. For that one needs about 12 gauge wire, compared to about 16 gauge wire that can be used for a serial configuration. The chip also would need to be considerably beefed up to handle that level of current, which doesn't make sense from an engineering point of view. Thus, if someone wants to draw 150 Watts from two batteries, to keep the current around 20A means using a serial configuration. That also means that the limit on parallel configuration at 20A will be at 75 Watts.