That sounds complex... while we don't have a hybrid model, I am sure that you could use the SDK for the native portion, then use a modified Web JS approach for that portion of the tracking... however, you will need to be careful to make sure that the two portions of the app interact properly together...
Make sure that you are passing information from the native portion into the JS portion (things such as the ECID so that you don't end up with two UVs and two Visits for each use of the app).
One thing that we do in our apps is ensure that each page in our mobile app is associated to a URL (either the equivalent to our website version of the page, or a "fake" url that represents the app)... While Adobe should just be looking at the timestamp of pages per user, if you are doing any sort of custom reporting that looks at referring data, you might need to pass information back and forth to ensure that this is captured in your tracking.
The best thing I can say is "Do lots of testing to make sure that the implementation is working as expected" and good luck.
Also, testing will be difficult, while you can use AEP Assurance on the native side (and look at the post-processed data), your will likely need a proxy setup (Charles or Fiddler) to test the JS portion. While the proxy will still capture the native portion, I would still recommend AEP Assurance to speed up testing where ever possible.