Можно ли расширить IEntityHistoryStore для хранения каждой таблицы, а не отслеживать все в одной таблице?

Да, из https://aspnetboilerplate.com/Pages/Documents/Entity-History#about-ientityhistorystore:

The Entity History tracking system uses IEntityHistoryStore to save change information. ... you can implement it in your own way ...

Реализовать MyEntityHistoryStore:

public class MyEntityHistoryStore : IEntityHistoryStore
{
    private readonly IRepository<zzLog.Tasks_Task> _taskLogRepository;

    public EntityHistoryStore(IRepository<zzLog.Tasks_Task> taskLogRepository)
    {
        _taskLogRepository = taskLogRepository;
    }

    public virtual async Task SaveAsync(EntityChangeSet changeSet)
    {
        foreach (var entityChange in changeSet.EntityChanges)
        {
            var taskLog = new zzLog.Tasks_Task()
            {
                TaskId = entityChange.EntityId,
                Description = entityChange.PropertyChanges
                    .Where(pc => pc.PropertyName == "Description")
                    .FirstOrDefault()?
                    .NewValue,
                // lgId = 0,  // Auto-increment
                lgAction =
                    entityChange.ChangeType == EntityChangeType.Created ? 1 :
                    entityChange.ChangeType == EntityChangeType.Updated ? 2 :
                    entityChange.ChangeType == EntityChangeType.Deleted ? 3 : 0,
                lgTime = entityChange.ChangeTime
            };

            await _taskLogRepository.InsertAsync(taskLog);
        }
    }
}

Замените сервис на IEntityHistoryStore в методе PreInitialize вашего модуля:

// using Abp.Configuration.Startup;

Configuration.ReplaceService<IEntityHistoryStore, MyEntityHistoryStore>(DependencyLifeStyle.Transient);