Bulk SMS has the option to select which number (from your connected phone numbers) you'd like to send from in the popout shown below.
But the Sequences, as they are based on Cron Jobs and such in the backend, it is hardcoded to send from the default phone number you have set in your account which will be the first number in your list.
At present how sequence sending for Bulk SMS works is that, if you have two connected Twilio numbers in the system, the sequence will always try sending from the very first number as we do not have any default settings for Twilio numbers within the system. We will be enhancing this feature by adding the ability to select the phone number to send from a sequence as well in the future.