Custom fields not shown on Step 2 of 'Merge Duplicate Accounts'

To display a missing custom field on the Merge Duplicate Accounts Step 2 screen, add the field to the Account Page Layout used by at least one of the records being merged. If both records use the same layout, add the field to that layout. If the records use different layouts, the available fields on the merge screen will be a combination of both layouts.

How to Edit the Account Page Layout

In Salesforce Classic: Go to Setup | Customize | Accounts | Page Layouts.
In Lightning Experience: Click the Gear icon, then go to Setup | Object Manager | Account | Page Layouts.

Scenarios

Scenario 1: When merging Record 1 (using Page Layout A) and Record 2 (using Page Layout A), the fields available on the merge screen will be all the fields on Page Layout A.
Scenario 2: When merging Record 1 (using Page Layout A) and Record 2 (using Page Layout B), the fields available on the merge screen will be a combination of the fields from both Page Layout A and Page Layout B. A field present on only one layout will still appear.
Note: In Lightning Experience, clicking Show All Fields displays all fields that the user's profile has access to via Field-Level Security (FLS), regardless of what is on the page layout.

For more information about Merging Duplicate Accounts, you can refer to this: Merging Duplicate Accounts.

See also
Page Layouts