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Yes, put the probe in the 1st chamber. The only benefit of the second chamber is to raise the ph. If your going to measure the effluent PH in a cup in the sump, then the second chamber really has no value. Unless for some reason you have a very small reactor, and your trying to add media volume.
Hmm lol I guess its not that hard to drill a hole in the first chamber and installing a "probe bulkhead" later on.
I bought plastic electrical cord grips for the diameter of the probe. They have 1/2" NPT threads on them. I still have 3 of these left, and the tap. Drilling and tapping acrylic can be adventuresome, just take your time.