Stil on same project where I had issue DI Registration service type .net core 3.0. Now when that is fixed I'm getting new error. Now my code looks:
    services.AddDbContext<ApplicationIdentityDbContext>(options =>
        options.UseSqlServer(configuration.GetConnectionString("Default")));
    services.AddIdentityCore<ApplicationUser>(options =>
        {
            options.Password.RequireDigit = false;
            options.Password.RequireLowercase = false;
            options.Password.RequireNonAlphanumeric = false;
            options.Password.RequireUppercase = false;
            options.Password.RequiredLength = 4;
            options.SignIn.RequireConfirmedEmail = true;
            options.Tokens.ProviderMap.Add("CustomEmailConfirmation",
                new TokenProviderDescriptor(
                    typeof(CustomEmailConfirmationTokenProvider<IdentityUser>)));
            options.Tokens.EmailConfirmationTokenProvider = "CustomEmailConfirmation";
        })
        .AddEntityFrameworkStores<ApplicationIdentityDbContext>();
    services.AddTransient(o =>
    {
        var service = new CustomEmailConfirmationTokenProvider<IdentityUser>(o.GetService<IDataProtectionProvider>(), o.GetService<IOptions<DataProtectionTokenProviderOptions>>(), o.GetService<ILogger<DataProtectorTokenProvider<IdentityUser>>>());
        return service;
    });
And error is:
System.MissingMethodException: Method not found: 'Void Microsoft.AspNetCore.Identity.DataProtectorTokenProvider
1..ctor(Microsoft.AspNetCore.DataProtection.IDataProtectionProvider, Microsoft.Extensions.Options.IOptions1)'.
I've had the same issue and the problem is related to the packages itself.
Basically the problem was that many of those Microsoft.AspNetCore.* packages are now moved to Microsoft.AspNetCore.App framework, so you remove your Microsoft.AspNetCore.Identity reference and add this to your project:
<ItemGroup>
    <FrameworkReference Include="Microsoft.AspNetCore.App" />
</ItemGroup>
I've noticed that my constructor (same as yours) is missing additional parameter ILogger<DataProtectorTokenProvider<TUser>>, which you can see in .NET Core 3.* versions on this link.
I ran into the same issue while creating a custom JWT provider for password reset emails. Instead of inheriting from DataProtectorTokenProvider<TUser>, I just implemented the IUserTwoFactorTokenProvider<TUser> interface directly. You will need to implement the CanGenerateTwoFactorTokenAsync method yourself but you can avoid the hacky framework reference.
From:
public class MyTokenProvider<TUser> 
    : DataProtectorTokenProvider<TUser> where TUser : IdentityUser
To:
public class MyTokenProvider<TUser> 
    : IUserTwoFactorTokenProvider<TUser> where TUser : IdentityUser
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