The real fix here is not to use the bold and italic shortcuts. InDesign works best, especially as your project complexity scales up, if you use defined styles for absolutely everything. In this case, create Bold and Italic Character Styles, and use those in place of any kind of override style, including the ones invoked by these shortcuts. You can reassign keyboard shortcuts to these styles if you really like (that is, if you find select/apply from the list too limiting).
It's important to grasp that InDesign is not Word (or any Word equivalent) and bad habits from using word processors shouldn't be carried over into InDesign projects. Don't use any kind of spot formatting — use Paragraph Styles for every paragraph, and Character Styles to apply different formats to parts of paragraphs. No exceptions.
Using styles consistently will let you do many things much more easily and with consistent results. As hard as it is to leave "typing" habits behind, it's a worthwhile effort to make.