This is a question that pops up frequently. In earlier releases of E-Business Suite, the rule was that you should never merge a patch with any of it's prerequisite patches. However, many years ago (I believe it was with AD_PF.E, but I could be mistaken), Oracle introduced the ability to merge a patch and it's prerequisite patches together. There are still a few (small) restrictions.
From the Oracle Applications Maintenance Procedures manual for Release 188.8.131.52 (Part No. B19299-01, pages 3-23 and 3-24):
In general, you can safely merge any Oracle Applications patch with any other Oracle Applications patch. Older split driver patches can be merged with newer unified driver patches. Patches can and should be merged with their listed prerequisite patches to make patch application easier.
However, patches that affect the Applications DBA (AD) product must be handled separately. AD patches can be merged with other AD patches, but AD patches and non-AD patches cannot be merged because AD patches may change the AutoPatch utility itself. Merged AD patches must be created separately and applied before you apply non-AD patches.
I believe you'll also find a similar statement in the 11.5.9 version of the document.
The primary logic here is this: If a patch says it requires a certain AD patch (say, AD.I.7), then what it's really telling you is that there is likely something in the structure of the patch itself that an earlier AD release wouldn't know how to properly handle. Keep in mind that AD patches are, generally speaking, patches to the patching tool.
Now, I have seen some patches that warn against merging. And, given the nature of ATG patches, you may be wise to exercise a level of caution and apply them independently as well.
The long and the short of it is, if you're reasonably current (certainly 184.108.40.206 and newer), it is generally safe to merge a patch and it's prerequisite together. Just pay close attention to the READMEs, and watch out for those AD patches.