Clearance hole, hole depth
You shouldn't need to edit that Excel document if all you want to do is make your counterbore or countersink holes not go all the way through. You should just be able to select the 'Distance' option, instead of the 'Through All' option in the 'Termination' settings of the Hole dialog box, after you have selected the hole type and seat type. What year/version of Inventor are you using?
Wesley Crihfield
(Not an Autodesk Employee)
I haven't ventured down that specific 'rabbit hole' before, but it sounds like a major time consuming project that would have to be custom to your needs. If you want main hole depths to be included within that Excel document, and you want a drop-down list of available hole depths to choose from after selecting the other sizes, you would have to exponentially increase the number of rows in the Excel chart (x number of additional rows for each existing row, depending on how many hole depths you want available), (plus at least one more column) then the existing Hole dialog still wouldn't use the new values, because it is not designed to. That dialog box is designed by Autodesk (background stuff that users can't really manipulate). You would then likely have to design your own custom Windows Form to use in place of the built-in one, so it would work all the new custom values and columns with your new Excel chart.
Wesley Crihfield
(Not an Autodesk Employee)
It's a little hard to explain. When one of us (users) creates our own VBA UserForm, or vb.net Windows Form, we have nearly total control over all aspects of its visible size and design, what data/content it will provide/accept, and how it will react to user interactions. We create all the code behind it, so we can specify where we want it to look for any externally referenced data, and what specific locations within those referenced data sources to get the target data from. A reference to an Excel file, can be set up to only look at a single specific cell address, on a specific named sheet, or it can be set extract the data from an entire column or row as a list of values to make available within a ListBox or ComboBox. It will always just retrieve that specific region of values from that specific sheet, in that specific file, that is in that specific location. A year later, of someone alters that Excel file, but doesn't update the code behind the form, the form is still going to be looking for the specific cell address, or that specific column for its data, and it won't know if any other new cells or columns exist, unless the form's designer changes the code behind the form to look in those different addresses for new data and how to use the data in those new locations.
But when dealing with a built-in dialog that was designed by some software engineer at Autodesk, we (the users) don't really have much control over that at all. We can't access its physical design specifications. We can't modify the code behind it. And we can't change how it will react to user interactions. All we can sometimes do is automate some sort of user interaction, such as a simple button click or simple keyboard entry. We (the users) can't change the design, functionality, or behavior of any of Inventor's built-in dialogs, unless Inventor has specifically included settings/options to allow that specific customization, because it is hidden in their proprietary software somewhere, and altering it is likely either illegal or would result in you loosing your license for using their software. You can request that Autodesk add this type of data to their charts and dialogs, and hope that they implement the changes in upcoming releases of Inventor, usually by creating posts within the Inventor Ideas site, but there usually has to be enough other people that agree with your idea and up-vote it enough to get Autodesk's attention.
If you still want to move forward with this project, I would suggest that you create a copy of the original .xls file to work with, while leaving the original alone, that way you can always restore it back to the way it was originally, if needed. You will likely have to name your new file exactly the same, and put it in the same location, while either renaming the original by adding something to the end of its name, or by moving it somewhere else temporarily, while you experiment with it. You may or may not have to close Inventor before saving edits to those files, because Inventor may be referencing them while it is open. There are undoubtedly some who have edited these files to add additional data into them, but mostly these edits have simply added more rows or changed existing data to customize the numbers to match their own custom fasteners. And I, as well as others, can and have accessed those Excel files through iLogic, VBA and other routes, because they are common Excel (spreadsheet) files and contain a lot of useful data.
Wesley Crihfield
(Not an Autodesk Employee)