300.5 is for where there is a change of temperature in a raceway run, such as at the service where a conduit is between the meter can and panel that is inside in a heated or cooled environment, in the OP case where the conduit and panels or junction boxes are all out side 300.5 would not have applied, and yes you would be correct, the sealing is only to slow down the transfer of air between the two points not to totally prevent it, all it is supposed to do is prevent moisture build up as the air changes temperature.
You mentioned 300.5, but I don't know if you were responding to my mention of 300.50(F) or not. If you were saying that 300.50(F) does not apply, I would like to submit that section 300 is "Wiring Methods", and 300.50 is "Underground Installations", and 300.50(F) is "Raceway Seal".
Where a raceway enters from an underground system, the end within the building shall be sealed with an identified compound so as to prevent the entrance of moisture or gases, or it shall be so arranged to prevent moisture from contacting live parts.
I would argue the lights are fed from an underground conduit system, and by the above mentioned code cycle they are required to be sealed. This section is not the one used for temperature difference, that one is 300.7, (at least the way I understand it).
If the conduits going to the lights had duct seal properly installed, I think there is a good chance this would not have happened. Since this was happening during/after a rain event, I would assume the water had something to do with it. If the conduit had 2' of cover, the pressure exerted by a 2' water column is right around 1 PSI. I would think well installed duct seal would be able to hold back 1 PSI of air pressure difference. The pressure was probably more than 1 PSI due to the ground resistance to gas escaping, but since this only happened when it rained, maybe the ground was not that much of a resistance.
Bottom line, I stand by my understanding that 300.50(F) requires these conduits to be sealed. I think this is a code section that is not enforced, just like 314.28 is often not enforced.