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I'm not sure this is a known feature, but apparently the marker size cannot be modified once created. As you can see in the screenshot below (edit of https://aladin.cds.unistra.fr/AladinLite/doc/API/examples/marker-creation/), changing the size (here from 18px to 40px) causes a shift in position.
You can also verify it live by loading the 3.8.0-beta version.
Possibly a different issue, but because the only difference between, e.g.,
cat.addSources(A.source(56.87115, 24.10514));
and
cat.addSources([A.marker(56.87115, 24.10514)]);
is the setting of the 'marker' option to true (options['marker'] = true; - https://cds-astro.github.io/aladin-lite/A.js.html#line234), I don't understand why for markers a popup inset is always shown when clicked.

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