Here the code:
from flask_sqlalchemy import SQLAlchemy
db = SQLAlchemy()
AvailableModules = db.Table('available_modules',
    db.Column('customer_id', db.Integer, db.ForeignKey('customers.id')),
    db.Column('module_id', db.Integer, db.ForeignKey('modules.id')),
    schema='tcloud_admin')
class Customer(db.Model):
    __tablename__ = 'customers'
    __table_args__ = {"schema":"tcloud_admin"}
    id = db.Column(db.Integer, primary_key=True)
    ....
    modules = db.relationship('Module', secondary=AvailableModules)
class Module(db.Model):
    __tablename__ = 'modules'
    __table_args__ = {"schema":"tcloud_admin"}
    id = db.Column(db.Integer, primary_key=True)
    ....
Trying the above script gives me this error:
sqlalchemy.exc.NoReferencedTableError: Foreign key associated with column 'available_modules.customer_id' could not find table 'customers' with which to generate a foreign key to target column 'id'
Without specifying the schema name everything works fine.