1) Where did Syndrome get his costume? Yes, he COULD have made it himself, but if there was, in fact, a "costumer to the stars" for the Heroes, Syndrome would know. And as a would-be hero, he'd go to her. And he's exactly the sort of guy to peeve Edna enough to get her to make him one WITH a cape.
2) Edna's dissatisfaction with the Status Quo is clear. "I used to design for GODS!" She's annoyed in the extreme.
3) Edna is a perfectionist. She COULD have repaired Bob's suit well enough to be unnoticeable even under pretty close inspection.
(one of the most telling points)
4) Edna didn't tell Bob about the tracking beacon. Edna knew that Bob was sneaking around doing Hero stuff. Unless she had ulterior motives she had no reason NOT to tell Bob about the features in the suits. Instead, WITHOUT telling him, she went ahead and made the suits for the rest of the family.
5) She was clearly WAITING for Helen to call. She could have called her any time, but didn't.
In my theory, this is what happened:
Syndrome finds Edna; convinces her to make him a costume, but makes such a pill of himself that she deliberately makes it with a cape, hoping something will happen to him.
Shortly afterward, supers start disappearing. Edna knows a lot of them even in civilian identities, obviously. Eventually she makes the connection.
Edna is already utterly put out that her entire career was derailed by stupid lawsuits. She wants things back the way they were.
So when Mr. Incredible shows up, clearly the next target of Syndrome, she finally has the perfect setup to put her plan into action. She knows Bob married Helen. She knows -- none better -- that the two have been trying their best to stay "normal". She also knows that with Bob keeping it secret, there is one obvious deduction Helen might draw from Bob's sneaking around.
So she doesn't tell Bob about the beacon or Syndrome. She sews the repair Not Quite Perfect and waits for Helen to call. She leads Helen to figure out Bob's been out behind her back, lying to her about the "job", and then hands her the tracker, knowing the family will confront Syndrome -- almost certainly publicly -- and usher in a new era of the Supers. And give her back her proper place.
All that has transpired here has done so according to my fabulous design, dah-lings.