Voting By Benefical owners

See, You have just confused,
In general sense, if you see Evey shareholder of listed company & companies who have demat their shares are Beneficial Owner (B/O)

What the beneficial owner provided u/s89 is beneficial interest, that's registered owner is acting on behalf of Registered owner (RO), For example, In Case of Wholly owned Private limited subsidiary, to comply with the legal requirement of 2 Subscriber ( 99% Shares are held by Company A and One share by Nominee of Company A), but during general meeting both the shareholder have right to vote but Nominee will cast his vote in a way in which Co. A want)

Further Section 90 ,It's SBO( Who holds indirectly holds >10% of voting rights) he need to give declaration in BEN-01 ,even though he has no direct right to vote or attend meetings

Related Party is not allowed to vote on any resolution and if they cast vote then will be considered as invalid ( except in a co. where 90% of members are related party or related to promoter or promoter group)

Coming to your point, only Registered owner on record dare has a right to vote on resolution and not of beneficial owner, but voting decision in all cases is generally of BO. If RO has appointed BO as his Authd rep or proxy then it's a different thing, else not.

one interesting thing, Evoting is done remotely where login details are provided to shareholder(RO) well in advance (21 clear Days), If RO who is in control of BO can share it's login details to BO and he can vote It without known by anyone.So,Such situation happens only when physically one is present in meeting