Yes, both of those launchers (as well as any others) will run "on top of" the skins, so you won't see any OEM customizations on your home screen. Customizations run well beyond "skin deep" in some cases, so you'll have to get used to other things being changed. For example, a few weeks ago I bumped up from a D1 like yourself to a DX. It has the lighter version of Blur. Some of the changes are as follows:
1. I can receive messages from Facebook in a threaded, handcent style fashion
2. I can sync my facebook contacts while having deleted the app
3. I can't control how many contacts are imported (on the D1 you can choose between none, only those already in your contact list, and everyone). All DX's are set to everyone.
4. There are subtle changes and rearranges in the settings screen. Thing are just labelled and organized different.
5. The buttons at the bottom of the phone are in a different, and have a different symbol.
6. There are different (and in the case of other skins, many more) things running in the background that you can't eliminate without root (even then, it's risky to go around deleting stuff)
I recommend going to the device sub-forums and inquiring about the good and bad of whatever phones make your "short list" to see what you can or can't live with. For whatever it's worth to you, I heard a rumor on one of the many podcasts I listen to.... I think this was from Engagdet Mobile... that the Droid 3 was supposed to be another Google Experience device. If you find out for sure that it is, you may want to hold out for that one if you can't find a tolerable skin.