Most 1990+ aluminum MC's were for power boosters (any production car w/o a booster since then?), so I expect no provision to lock the pedal rod. But, I did a test-fit of the rod in the Neon MC, using a new rubber bushing (for 1964) on the end of my 64 pushrod, and it fit tight. I then decided to add a rubber dust boot, so removed the rod. I had to beat it out, which tore up the rubber bushing in the process, so I would say it locks into the piston very well, just like in my original 64 MC. Forgot where I bought the bushings, maybe ebay or Booster Dewey.
Regardless, it seems the only way the rod might fall out of the MC would be if the piston hung up in the bore so that the return spring couldn't push it back. The driver would notice the pedal not coming up and have to pull it up. With the rod locked in, that might slide the piston back. If the rubber bushing didn't hold, the piston might stay hung-up and perhaps there is enough clearance for the rod to pop out, but your MC is toast either way. In such an emergency scenario, instead of fooling with the pedal, I would downshift to "1" and go for the e-brake. I use silicone brake fluid, so everything stays pristine inside and can't see my MC piston sticking.