Vanilla overlays are supported by ItemsAdder.
You can create your own pack.mcmeta and put your overlays entries there.
ItemsAdder will merge them all into the resulting pack.mcmeta of your pack .zip file.
Minecraft Wiki information
Pack format version for each Minecraft version
Example
contents/myassets/resourcepack/assets/minecraft/pack.mcmeta
{
"pack":{
"pack_format":63,
"description":"My Pack"
},
"overlays":{
"entries":[
{
"directory":"my_overlay_1",
"formats":[
42,
43
]
},
{
"directory":"my_overlay_3",
"formats":[
44,
47
]
}
]
}
}