I would think about applications through 2 channels: JOE and non-JOE
If you're applying through the JOE - great! Your resume will likely get at least a 30 second review. That's way better than nothing.
If you're applying through a non-JOE channel, you're not even guaranteed that 30 seconds.
I can't stress enough that applying via an online job portal (or any other electronic method) is, by itself, usually a dead-end. Here are some reasons why:
The convenience of electronic applications means that there will be a flood of applications. You might not be looked at.
In order to handle the high volume of applications, recruiters will usually use some incredibly bad automated resume processing tool (note: these are all bad, because the outcome-matched training data is insufficiently sized relative to the highly diverse and unformatted feature space) to filter resumes on some sort of best matching function. Even if you have a well-designed resume with great keywords (python, machine learning, etc.) you might not be looked at.
If you're applying to an online job posting, it may already be filled. You'll definitely not be looked at.
If you're applying to an online job posting, it may have been posted only to satisfy non-discrimination laws while the hiring manager hires an internal (or, in some cases) external candidate they already know. You'll definitely not be looked at.
For these reasons, the "send and pray" online application strategy is a last resort. Look for managers at the company on LinkedIn - many of them will say in their profiles they're hiring, which is a license to contact them. Reach out to people with a role similar to the one you're applying for and see if you can get one of them on the phone. As discussed in the "Networking" section, it's better to do this before you're applying, but you miss 100% of the shots you don't take.
Whether you're applying through the JOE or another channel, check to see if you, your advisers, your friends, or even an acquaintance knows someone at the firm where you're applying. If they do, ask them to reach out on your behalf to their contact at the firm. If you're applying for one, two, or three hundred jobs, then you have to be selective about this, unless you can find a separate proxy to advocate for you with each firm. But if you can find a contact at the firm that either knows you or someone in your network, you will greatly increase your odds of getting an interview.
Finally, if there's a firm that you really want to work for who has a JOE ad, you can still reach out to hiring managers at that firm on LinkedIn. It certainly happens that you'll get noticed in one channel and not the other, so there's value in applying through multiple channels. It also signals extra interest; I've seen us interview candidates we'd normally pass over because they reached us through non-JOE means. However, if you do get responses through both channels, just let everyone know as soon as possible. The firm will be happy to find the best way to interview you, and maybe even interview with the team you find most interesting.