I'm not sure what you call a dynamic smartlist. In an MC context, so to speak, a smartlist is dynamic by nature.
MC 11 has a 'sync data' option (it sync 'last played' and 'number of plays' with the iPod. If you use that option, here's what will happen in your example.
Let's say you create a 'Top 25 Most Played' smartlist in MC. You synchronize that playlist with iPod. You play some of the songs in that smartlist on your iPod. Please note first that the playlist is not dynamic on the iPod, i.e. you can play a tune as much as you want, it will always remain at the same place in your iPod 'Top 25 Most Played' playlist. That is, until you sync with MC. When you do this (provided you've selected the 'sync data' option), your playcount is updated in MC, and thus, your 'Top 25 Most Played' is updated as well (since it's dynamic). It is then (during the same sync) re-transfered in its new state to the iPod.
In a way, MC still overwrite and destroys these 'smartlists' on the iPod, but the process is transparent and the result accurate.
What I'm not sure about is what happens if you play a file several times on the iPod. I seem to remember that I read somewhere that the Ipod didn't keep an actual playcount, just the last played info. I'll try to play a file twice, sync with MC and see if the playcount in MC is accurate afterwards. I'll keep you posted.