I am hitting a similar problem and if I understand correctly it seems this is specific to multisite configuration. For multisite the multisite:migrate occurs in the hook after_bundle_exec but the assets:precompile is trying to do its thing for each db configured. Meaning, for multisite the db migrations are actually happening after the asset compilation.
At least that is my guess!
The best solution I could think of was to edit web.template.yml to perform the multisite:migrate directly prior to assets:precompile. This works for me temporarily at least.