The paper shows that 95% of cell phone subscribers are personally identifiable from VERY little spatio-temporal information.
Another issue is that an upstream vendor could easily provide the government with the phone IMEIs and SIM IMSIs that they supply to BurnerPhone, without disclosing this to BurnerPhone. This would create a pool of phones that are self-identified as high-value surveillance targets.
If I was in charge of identifying miscreants for a nasty regime, I'd also watch for SIM card changes (an IMEI whose IMSI changes on a regular basis), and I'd especially look for cliques of handsets that showed the same SIM-changing behavior. As such, I can't help but wonder if swapping SIM cards might generate unwanted attention.