I believe it should be possible to have the RX and TX counters synchronized +/- 1 clock cycle.
There is a single timestamp enable bit from the FX3 -> FPGA that is turned on with the first bladerf_sync_config() call that enables timestamps. This implies that you'll want to have the sample rates already setup up before your bladerf_sync_config() calls (for either module), otherwise your counter would have drifted since it was operating at a different rate for some amount of time.
It sounds like you're working on some sort of TDD application? If your uplink and downlink are on the same frequency, I would advise you to ensure the RX and TX frequencies on the bladeRF are tuned at least 1 MHz apart, and digitally mix to the target frequency. I say this because we've found that if the PLLs in the LMS6002D are tuned within 1 MHz of one another, they may begin interfering with one another.
Fortunately, with 28 MHz of RF bandwidth, there's plenty of room to simply mix either RX or TX.

Best regards,
Jon