Joemt,
You ask a good question. Since TRL does not provide any details of their mods it might be difficult for me to get any more information. However, when I got the original modified unit Paul Weitzel told me I'd be much happier with it as a transport.
Now, the latest mods for the Alesis focus on making it a much better CD dupplication/recording tool. TRL uses the Alesis for their 2-track masters on their recording labels. They are on a mission to make the Alesis the best CD duplicator and recording unit. I'll be sending mine in for the new upgrade. If you are using a stock Alesis you may want to consider the full TRL upgrade package at $550 which includes the new mods that I will be getting. It will take the Alesis to a new level and make it an excellent CDP as well (which like me, you may or may not need, since youre using a DAC, but the option is nice for me as my DAC is non-os and the Alesis CD will give me upsampling options).
I realize the Alesis does not have the flexibility of the Squeezebox, but I'm not yet convinced that the Squeezebox device is the answer to hard drive digital playback. I think we are at the tip of the iceberg right now with this type of technology and better options are on their way.