If your trigger email notifications are landing in affiliate spam inboxes, chances are that you may need to set up a Sender Policy Framework (SPF).

This ensures maximum deliverability of emails, and adds a personal touch to your affiliate marketing program.  

Your developers can set that up for your following this guide.

Larger domains typically will be using a DMARC record to add an extra layer of protection. If this is indeed the case, DMARC validation will fail due to misalignment of your 'from' domain and the d= domain. 

In this case, a possible solution is to send emails from a subdomain (e.g. @affiliates.your-domain.com), create the appropriate SPF record, and then create a more relaxed DMARC record, specifically for that subdomain.