Yes, those are the shortcomings of InDesign. Concerning PAC: you should differ between the warnings under 'Quality' and the two 'pdf/ua' and 'WCAG'. The errors on 3 and 4 for example are under 'Quality', consider those as hints on 'could be better' but you can ignore those. Concerning Alt text and note ID, those can be fixed with Acrobats Preflight single fix actions. For point 5: InDesign puts the text under Note in a P-tag, just drag it out of the P tag (delete the empty p tag) and directly under the Note tag.
It is InDesigns limited support sadly enough in its export.
To prevent most of those errors, take a look at the MadeToTag plug-in, it is a must have when dealing with Accessible pdf.
That said, there is no use in @Abhishek Rao looking into it as this is just the way it works in InDesign.
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