Measuring at 1000 Hz is kind of tricky: it works in some cases, but even wire would resistors can be a problem. Measuring with AC is not that bad (as this allows for better amplification), but a low frequency (e.g. 10 Hz range) would be preferred. This would also allow to generate more current from a battery using a transformer.
Using 2 ADC input channels in the DIY solution is not that bad. It is a little slower and might suffer a little from current drift, but it eliminates ADC gain drift and allows for a low voltage for the reference resistor too. With something like a 10 or even 1 Ohms reference resistor to compare with, it is hard to get a suitable voltage without a high power resistor.
The main problem is not having much protection. Not sure how the readings are taken in the SW, but the HW at least allows for reversing the current and even working with a reduced current for slightly larger resistors.