Hate to say it, but at the time when that was made, a pH probe holder in the lid was an extra cost option. No reason other than that. The first to buy that reactor did not elect to pay the extra $20 or whatever to get a probe port put in the lid.
How do I know? Because I had MRC do that when I bought my first calcium, reactor from them in 2008.
You might contact SEA and have them put a probe holder in the lid for you, or just use the cup option you mentioned. They both work the same. You could also DIY it...shouldn't be that hard. MRC has gone to retail only to the best of my knowledge, so you have to go through a LFS now.
Actually, the DIY way might not be too easy. IIRC, the probe holder is threaded, so it is not s simple drill and glue deal. The lid hole needs to be threaded, I think. May be something to have SEA do for you.