Currently, internally items and stacked items are treated as separate Items. I'm are exploring an option to allow inserters to use these items. An approach could be to create recipes that accept stacked items. This has not been fully explored yet, as it might introduce additional gameplay complexities, such as needing to select different recipes making extra steps for the player. For instance, furnaces could potentially accommodate this system without requiring players to select specific recipes as they do not require recipes to be selected. Regarding the issue when switching items there is a internal inventory that changes the items to be stacked if there is still items new one can not be accepted several solutions are being considered. Most of them involve runtime scripts, which I'm trying to minimize due to performance concerns.
Thank you for the message let me know if you find anymore issues!