There are multiple facets of tax-compliance strategy involved in the raised query, where every factual aspects of the business to be considered before answering the issues like subject queries.
In other words, it would be risky to answer the queries without knowing multiple factual aspects of that particular business and tax-compliance strategy structured to minimise areas of disputes with Dept. as well as to minimise potential losses of ITC (if any) and to maximum maximum efficiency through tax-planning.
Broadly specking, following facets needs to be looked into:
A. Whether said tax-payer have 'fixed establishment' in other states / UT where employees are stationed? And yes, regular registration in other states / UT becomes compulsory.
B. If said tax-payer do NOT have 'fixed establishment' in other states / UT where employees are stationed & there is no need to take regular registration in other states / UT, whether 'casual registration' - which is compulsory - comes into picture?
C. And Co. has indeed taken / will be taking regular registration (or, casual registration) in other states / UT, what type of services are provided from these registrations to its HO / manufacturing location etc. (For example: Marketing & Support) OR any outward supply to third party gets created (if any) and how any of these outward supply and liability thereof can be structured. And there is any 'additional' loss of ITC involved due to any of planned business structuring - for a Co. as a whole? Depending upon answer to these questions (i.e. tax compliance strategy taken for Co. as a whole), answer to the query raised by you should be looked into.
D. If said tax-payer do NOT have 'fixed establishment' in other states / UT where employees are stationed & there is no need to take regular registration in other states / UT as well as 'casual registration' is also not applicable, then, answer to the query raised by you may be materially different than the situation where these registrations become compulsory.
E. Many facets relating to use of ISD mechanism (even when compulsory) is also inter-linked with entire tax compliance strategy and cannot / should not be looked into isolation.
These are ex facie views of mine and the same should not be construed as professional advice / suggestion.