I dont know what their stance on Transformers customs is, but the official Hasbro GI Joe custom guidelines can be found here:
http://www.hisstank.com/forum/g-i-joe-news-rumors/5076-hasbro-provides-customizing-guidelines-collectors.html
basically says:
1. Hasbro encourages the customizing of individual figures for personal usage, and can be resold as one-of-a-kind, out-of-package figures.
2. All Hasbro artwork, such as card art, cannot be reprinted without permission from Hasbro. These assets contain Hasbro-owned trademarks and logos, and cannot be sold or reproduced without Hasbro's permission
3. Hasbro owned trademarks such as character names and the GI Joe brand name cannot be used without written permission from Hasbro.