You can replace the metal core plugs with the rubber ones, they are much easier to install in tight places.
Factory uses the metal ones because they are much much cheaper to install when building the engine from scratch.
And no, engine won't get damaged from possible freezing with rubber plug.
"freeze plug" name was given to the core plugs prior to anti-freeze being used.
In the winter you had to drain the block if temps would be going below 32degF
If you didn't and water in the block started to freeze a few of the core plug would be pushed out, but...............water in the lower block could still freeze and crack the block.
So they are not there to prevent damage from freezing, they pop out when water freezes, they are there to get the sand out of the block(core) after molten metal casting