Yes, the slow speed (4800 or 9600) of the serial comms links many receivers use worried me and I know that several that are ostensibly USB actually use a USB/Serial interface internally and so are just as bad. I noticed that to get round this the NMEATIME2 shareware uses a Kalman filter to filter NMEA arrival times and manages to get an accuracy down into the single milliseconds.
I’m told – would have to check old emails for detail – that the 1pps is very accurate long term (so count 100 pulses and the average interpulse time will average very close to 1000ms) but the individual arrival time of a pulse is still somewhat dithered – on some hardware.
Can dig out the emails if you are interested.