Yeah, Indesign doesn’t handle custom cell format very well… (euphemism…)
What I would do is to forget about Excel custom cell formatting and use an Excel function to turn the number into formatted text.
Maybe the easiest way would be to create a new sheet and to use a function to get the real values from your working sheet while turning them into formatted text.
Then, in Indesign, tick “import options” and select that new sheet.
I guess the “TEXT” function is the one you are looking for.
See : https://support.office.com/en-us/article/text-function-20d5ac4d-7b94-49fd-bb38-93d29371225c
Type
=TEXT(YourWorkingSheet!A1;”#,##0.00 “)
in A1 in your new sheet and copy/paste in order to duplicate your working sheet.
If your table have always the same number of cells, it should be easy enough
If not (e.g. you have to add/delete rows from time to time), then you’ll have to deal with empty cells.
This would be more a call for an Excel forum…
Please note I use a French version of Excel. So I tried to “translate” the function, assuming you have an English version, with a comma as a thousands separator, and a dot as a decimal separator. But I could not test it properly, so hopefully it will be ok.
Hope that helps
Vinny