try not to use expanding foam unless you have to, and then only use it for places you can't reach with other forms of sound damping materials. If you used matting on the trunk lid, that should absorb resonance, and lower the sympathetic frequency of that piece of metal enough to be effective. If there is anything that's still ratting excessively that you feel needs attention, then you could consider the use of foam as needed.
I would suggest using foam in your trunk lid. Do it in layers and not all at once or you will have an issue with body bulge. Not sure why you wouldn't want to use it. Lighter, works more efficient, and can get into spaces you can't.
Definitely take your time and do foam in layers. I did 15+ cans in my rear tailgate (tahoe) and it's like a rock now. Extremely solid, and by doing it in thin layers I got nice expansion without bowing my panels out.