[SalesForce] Currency is coming as Standard field in every custom object

Short answer: you can't do this without a major investment.

Longer answer: my job is developing FinancialForce's PSA application, which requires supporting dated exchange rates and other ACM features on custom objects. Salesforce has confirmed to us more than once that there is no native way to do this, so we've implemented our own currency conversion from the ground up to support our needs. We do support reading the dated exchange rates from ACM's tables, but we still have to do all our own math on the conversions in apex logic. At the very least this means that you can tap into the same currency data for your calculations, even if the implementation of the logic must be done independently.

The net effect is that if you want ACM functionality outside of the officially supported objects you're going to have to build you own currency conversion system, and your own apex-managed rollups rather than using the native functionality, for this to work. If you do go this route you'll probably want to turn off parenthesized currency conversions as they'd use the non-dated rates and effectively lie to users of your custom currency system.

This is obviously a non-trivial solution to the problem, but it's the only one that's currently possible today.

Once multi-currency is enabled in your org, most objects in the database now have a CurrencyIsoCode field on them. Just because objects like the Opportunity object and your custom object are related by a lookup or master-detail, does not mean that the CurrencyIsoCode codes will be the same. These are separate records in the database, with separate CurrencyIsoCode fields. It sounds like your custom object record has a CurrencyIsoCode in USD. If you change it to CAD, then it will render the currency field in the same format as your Opportunity.

You might consider a Visualforce page for the new and edit screen of your custom object if you need to keep the currency sync'ed to your Opportunity.