Hi,
You are correct. You should not define any other transaction log backups outside of the Log Shipping configuration, in order to ensure that you maintain the natural Log Sequence.
Should you however wish to perform an Ad-Hoc transaction Log Backup, heaven forbid because you are performing some live maintenance on the production database for example, then you can call the SQL Server Job that Log Shipping uses to perform your transaction log backups. It is typically called LS_Backup. This will maintain the LSN.
To my understanding, no operational features of the database being Log Shipped are limited by using this availability technology.
Some things that can cause complications:
Encryption
If you are log shipping to another server and are using SQL Server native encryption then you will not be able to access encrypted data within the log shipped database unless SQL Server is using the same service master key.
Assemblies
You may experience difficulties accessing signed assemblies within a log shipped database, as you cannot enable the trustworthy property.
Permissions
If you intend to provide read access to the Log Shipped database then the SQL Server Logins will need to have the same SID as those from the source server in order for the logins to automatically map correctly.
Hope this helps. Cheers.