MySQL GTID replication: is it possible to make DDL changes to a slave and then catch it up to a master?
You have described a common way to make DDL changes.  Yes, it should work.  But...  please describe the datatype change further.

If you are ALTERing a COLUMN that is current INT SIGNED to be a SMALLINT SIGNED, and if none of the values are bigger than 32767, there should be no problem.  If you are changing from SIGNED to UNSIGNED, and none of the numbers are negative, then no problem.  Etc.  In general, if the old value will fit in the new datatype, then it is OK.  If it won't fit, then something will be lost.  1 million into a SMALLINT UNSIGNED will probably become 65535.

As for the application, how does mysql know it is getting an 11-digit id?  It sees a number of some number of digits and shoves it into the target size.

Do SHOW WARNINGS; after the DDL.