Overlay + matte?

we can’t layer both an overlay and a matte transition can we?

Yes, you can combine overlays (QuickTime mov with alpha) and luma mattes to create some cool effects. Here is a really simple example using an overlay animation followed by a luma matte. The overlay plays a fraction of a second ahead of the matte:

{
    "timeline": {
        "soundtrack": {
            "src": "https://shotstack-assets.s3-ap-southeast-2.amazonaws.com/music/unminus/palmtrees.mp3",
            "effect": "fadeOut"
        },
        "background": "#000000",
        "tracks": [
            {
                "clips": [
                    {
                        "asset": {
                            "type": "video",
                            "src": "https://shotstack-assets.s3.ap-southeast-2.amazonaws.com/overlays/arrow-overlay-orange.mov"
                        },
                        "start": 2.6,
                        "length": 2
                    }
                ]
            },
            {
                "clips": [
                	{
                        "asset": {
                            "type": "luma",
                            "src": "https://shotstack-assets.s3.ap-southeast-2.amazonaws.com/luma-mattes/single-arrow-right.mp4"
                        },
                        "start": 3,
                        "length": 2
                    },
                    {
                        "asset": {
                            "type": "video",
                            "src": "https://shotstack-assets.s3-ap-southeast-2.amazonaws.com/footage/table-mountain.mp4"
                        },
                        "start": 0,
                        "length": 4,
                        "transition": {
                            "in": "fade"
                        }
                    }
                ]
            },
            {
                "clips": [
                    {
                        "asset": {
                            "type": "video",
                            "src": "https://shotstack-assets.s3-ap-southeast-2.amazonaws.com/footage/road.mp4"
                        },
                        "start": 3,
                        "length": 4
                    }
                ]
            }
        ]
    },
    "output": {
        "format": "mp4",
        "resolution": "hd"
    }
}

This is the end result: