It is strongly recommended to gather stats on the custom schema especially if there are lots of data in its tables.
Check this document:
How to Gather Statistics on Custom Schemas for Ebusiness Suite 11i and R12? (Doc ID 1065813.1)
agree, if you want, can use backend procedure to gather Custom Schema Statistics
exec fnd_stats.GATHER_SCHEMA_STATS('<CUSTOM_SCHEMA>',10); -> 10 is gather percentage, you can use other number also based on requirements
Gather stats can be performed at data and index level as well, make sure you are not running at Business peak hours. There could be possible performance deviation.
As suggested above by Amit, the percentage might be different., depends and the amount of data you have.