Nope, you are forgetting to acknowledge the sentance before the one you quote.
As noted, they are queued. As we know, eggdrop queue support flood protection. This is where is the reason behind modes not being sent. It should probably read "sent as soon as possible" though.
If there is a real need to bypass the flood protection of the queue system, you can use the non-documented putdccraw command. It is very simalar to putdcc, but has 1 extra requirment, and 1 extra function.
putdcc uses the format
putdcc <idx> <string>
While putdccraw uses
putdccraw <idx> <string> <length>
You are required to pass the length of the data you wish to send. In most cases, a Tcl "string length" will be enough.
The extra function, is that you can use a IDX of 0, to send to the currently connected IRC server.