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I always make my PCB such that I can program the parts in circuit.
It also makes code development easier since you don't need to remove the part to reprogram.
Not to belabor this, but: Put .020"/.5mm holes where you need test-points or programming access, then populate one of your PCB blanks with these spring-pins: https://www.digikey.com/product-search/en?x=0&y=0&lang=en&site=us&KeyWords=ED90384-nd in those positions. This gives a perfectly-aligned bed-of-nails fixture, and the pins will (just) fit in a 2mm grid.You don't need space for a connector. Just a few bare pads that some spring pins can touch. I usually put them right under the uC on the bottom side of the PCB.