Hi Romain,
Yes, the RTI can be used as wake-up source from STOP1.
Below is an example of initialization to use the RTI as wake up source from STOP4 or STOP1:
// First clear flag
SRTISC_RTIACK = SET;
// Select LFO as clock
SRTISC_RTICLKS = CLEAR;
SRTISC_RTIS = period; // where period takes one of the values specified in Table 24
// Enable interrupt // No effect for wake up from STOP1
SRTISC_RTIE = SET;

It is correct that upon wake up from STOP1 on RTI interrupt, there will be no associated flag in TPMS_INTERRUPT_FLAG or SIMSES register.
This fact can be used to determine if the wake up from STOP1 was due to RTI or not; for example the following can be done upon wake up from STOP1: if SPMSC2_PDF is set, TPMS_INTERRUPT_FLAG and SIMSES are clear and RTI interrupt was enabled before entering STOP1 (this information can be stored in a variable in the PARAM section) then the wake up was due to RTI and the specific process can be executed.
Best regards,
Tomas