Sektor is an interesting assist in general, I definitely think the versatility of Missile ambush can pair well with Reptile's overall versatility.
There are numerous timings you could employ with F32 and Rocket ambush, in fact, I would encourage you to mess around with different call timings both midscreen and in the corner to get a feel for how the assist works. Here's a simple example off of F32xinvis, you can call missile right as Reptile's claw makes contact with their stomach, this will make the missile hit them just as they're waking up, allowing for a simple armor break paired with something such as B3.
Another interesting setup would be calling missile right as you visually see Reptile begin the invisibility animation, where he "Vomits" over himself, and then meaty with B31. This timing will cause the missile to hit right after the 1 of the B31 lands, if they D1 or input a string, the missile will grant you a full punish off the hit stun. That being said, the weakness of this assist is in the lack of frame advantage it provides, it very much relies on your opponent's impatience and willingness to mash on wake-up rather than to simply block.
Further, you do not have enough frame advantage to do anything more than D1 if they block the missile. I'm not sure if anyone has actually calculated the frame advantage up missile has, but the opponent recovers so quickly I have a difficult time believing it is anything more than one frame of advantage. However, now that you have them conditioned to block after B31 you may begin trying other things, such as simply doing B3 into a micro backdash to gauge their reaction. Are they respectful of this change? Do they still D1 at a similar timing? Do they forward dash? Do they reversal? Maybe you slightly alter your call timing so that now the missile hit slightly before the 1 of B31 to armor break, or even later than the initial setup I told you.
This is a very lab-heavy assist, do not look at it as a simple frame advantage hog, you can't necessarily call it on the fly like you can with Kano's knives, Stryker's grenades', Goro's Up Punch, or even Cyrax's horizontal chopper, there's too much startup and too little advantage for that. But you CAN use it to surprise your opponent given that this is an assist that comes from a vertical, aerial approach, rather than the horizontal one the other assists do. It can be difficult for the opponent to understand WHEN the missile will actually hit during knockdown situations because of this, which is why you should play around with different timings and strings, in order to throw them off. You may call it midscreen after ending a combo with fang drop, forcing the opponent to block on wake-up fullscreen, and allowing you use MB slow Forceball to encourage your zoning game.
Or, you can call it during the invisibility animation in the corner, which allows you to get a full combo off forward throw, and results in invisibility setplay on F32 knockdown given you'll be fully invisible by the time you end in that string. Look at his other assists, the quick teleport punch may not give you a full combo fullscreen on hit but it DOES allow Reptile to elbow dash in and meaty them. The buffs to flamethrower also compliment you from a neutral and pressure perspective, opponents will have other layers of space control to worry about in addition to your forceballs. Experiment with him, he may not be as immediately effective as Stryker in terms of ambush offense, but he can definitely throw people off online.