If you are interested in knowing conceptually, here are the implications that i can foresee.
a) Table column added using alter table is virtually useless as the application wont be able to use it because its definition is missing from Siebel Repository.
b) If you change the length of an existing column, application would still be using the length mentioned in Siebel Repository.
c) EIM process will ignore your new column length as it loads data dictionary before running the job.
d) And finally, during code migration you have to do the alter table every time since DDLSync process cannot take care of your scenario.