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Even though meta-intel has support for the Galileo as stated in the Yocto Website, there might be some incompatibilities using Jethro. What is important to check is that the layers you plan to add need to be compiled for the same version as the one ones of this release. That’s why even though new versions appear, the recommended BSP to follow is the one posted in the Galileo downloads website or http://iotdk.intel.com/src/3.5/galileo/ . This last link is the BSP for the eglibc image.
You can use split layers but again, make sure you’re using the same Yocto version for all layers. You can check https://software.intel.com/en-us/blogs/2015/03/04/creating-a-yocto-image-for-the-intel-galileo-board-using-split-layers for a tutorial on how to create an image for the Galileo using split layers.
In case of the Arduino sketch functionality, as you said the important file to notice is meta-intel-galileo. If this layer is compiled in the same version as older versions then there should be no problem with older releases that are also compiled for the same version.
I'll give it a try with Daisy branch (since meta-intel-galileo requires layers from this branch) and post my results.
Again, thank you for the great explanation.