The downside to your modification is that if lines come 3 per second, you still only read one per second. And if lines come one every 2 seconds, your alarm has even odds of not doing anything.
I also think that the emulation can be fixed. Just use a select/sysread loop, which gives you lots of opportunities to be interrupted. Yes, it is a busy wait. But if you only do it when there is an outstanding alarm, I think it is a reasonable tradeoff.
In fact it is even possible to make that fix in pure Perl. All you have to do is tie the filehandle to an implementation that has a READLINE that does the select/sysread loop and returns when it completes a line of text. (Don't forget to strip out "\r".)
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