Hi Ivan
I went through a similar topic some time ago. The answer is: generally speaking, no. The tools you mentione target specific protocols, which are a few (ip/tcp/udp ecc), but the cover the majority of traffic. To go to upper layers you should know the semantic of the protocols you want to anonymize. Moreover, not all fields are straightforward to change. A 4 bytes integer can be, a string, whatever its format is, is not straightforward (you could go to a change in packet len, then lengths have to be changed, etc.). And that's not all: the fields you're changing could require changes in other fields. A stupid example: a protocol with an IP + a flag that indicates whether the IP is from net 10. would require to change both.
If you want to target a specific procol, you should write a software that knows that protocol and that does the dirty work for you.
Tracewrangler is the most advanced I know, but falls in the aforementioned category.
Bye.
Dario.