Sounds like you are doing what you need to do. As long as the drain holes are open, you should be fine. Our field Meyers and my few container Meyers get rain every day for 6 months; they do fine, but they actually grow more in the drier seasons, as the roots have to grow to seek out food and water.

I have experienced that rain on potted plants seems to be fine. I have not lost a potted plant yet from outside rain

I worry that these citrus need drainage. My passionflower is loving the rain, of course.

I deal with excessive rain with one of these.

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6b Steve

You could tape plastic/foil around the plant base and over the pot to prevent rain from going into the pot if you're expecting excessive rain. If your pot with 2" water wasn't during a super heavy monsoon, you probably need to improve your drainage. It sound like you have either or a combination of really poor and compacted soil o obstructed drain holes (perhaps a completely root bound plant which could obstruct your drain), you could drill holes like Steve has in his pots as a temporary improvement for drainage and aeration until you repot.

My experience, I've only had standing water in the top of a pot when I had a root bound pot. I had to drilled some holes temporarily.

Good luck.