Quoting some text from the refrence provided by you i.e.
https://www.taxsutra.com/content/has-govt-notification-unintentionally-restricted-depreciation-rate-40-all-taxpayers
"The Rule 5 has been amended w.e.f. April 1, 2016 and inserts a new proviso restricting depreciation allowance to 40% in case of domestic companies opting concessional taxation under newly inserted Sec 115BA. Finance Act, 2016 introduced Sec. 115BA............."
"Based on the overall 'spirit' of the notification, the intention seems to restrict depreciation only in respect of companies covered by Sec 115BA. However, a strict reading suggests otherwise. Hence, a clarification on this aspect from the CBDT would be immensely helpful."
"To amend the new Appendix IA read with rule 5 of Income-tax Rules, 1962 to provide that highest rate of depreciation under the Income-tax Act shall be restricted to 40% w.e.f 01.4.2017. (i.e. from previous year 2017-18 and subsequent years). The new rate is proposed to be made applicable to all the assets (whether old or new) falling in the relevant block of assets."