how can I alter the way which the Digi TS16 assembles serial data to avoid payload split between IP packets?

It is not possible to control the packet size with these units as they service the serial port data on a polling basis. You can lower or increase the polling rate using the optimize setting:

This can be configured using telnet or SSH to the connect to the unit, logging in as root and issuing the following command:

#> set config optimize=latency

This will increase the polling rate (putting higher load on the network).

#> set config optimize=throughput

This will decrease the polling rate.