There is a stark difference in having some chakra, and eating a part of the beast's flesh. One instance, Naruto has the whiskers as a result of having the Kyuubi's influence since birth. Kinkaku and Ginkaku actually consumed the beast's flesh and gained a portion of its ability. Naruto's ability to transform is only due to the Kyuubi still being in him. Now, the flesh K/G ate is an actual part of them. So they can go V2 w/o Kyuubi actually being inside them, but Naruto cannot.
*Might I suggest that the whiskers you saw on Naruto's baby face was left over influence from the beast and nothing more. If he hadn't have been a jinky since that day and on, then the whiskers would have just gone away. Notice that neither Kushina nor Mito had this effect. Since Naruto was so young it DID alter his DNA slightly, but not on the level of Kinkaku or Ginkaku.