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I have figured out the anwser myself so I hope it may help others in the future.
The issue was mainly that I was not using a launch file and didn't set the "use_sim_time" parameter using rosparam set manually before launching my nodes. Doing so can solve the issue or should at least make the timestmaps be much closer to each other (i.e. the seconds should be the same).
Another thing is making sure the listener has enough time before a transform is requested. In my case I simply put a 1 second sleep before the start of my loop. Publishing a transform every 100ms may also be not sufficient depending on your parameters that may be a problem. However if the sim time is set properly and the listener had some time to fill up with transforms there should be only a couple of error messages if the frequency is not high enough so it is fairly easy to see.
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