You can break the question and solution down into two parts. The first is whether the UPS Pico has sufficient current capacity to power both the Pi and HDD concurrently. The concern is current, not voltage. A quick check on the Pico description indicates it comes standard with a 450mAh LiPO battery which can be upgraded to a larger 3000mAh (you should be able to upgrade the battery to any current capacity within the rating of the Pico). So you need to determine your max current draw from the Pi and add the max current draw from the boost converter/HDD. Then figure out if your battery can supply enough current to satisfy both of them for the length of time you need them running on UPS battery standby power.
The second part, which is really more of a concern that needs to be considered, is the potential for data loss on the HDD during the momentary transition from regular power to standby power. If the HDD is writing data at the moment the power loss occurs, this "hiccup" might create a data integrity failure that corrupts your HDD filesystem (it's possible a similar filesystem problem could occur on the RPi SD card if it were also writing at the same moment).
The part of this I'm not sure about is how seamless the power transition is on the Pi when the UPS Pico takes over. If we ASSUME that it is nearly seamless (no hiccup), then a solution to ensure a smooth transition for the HDD might be to always power the HDD from the boost converter connected to the 5v GPIO pin on the Pi. This way, there is no power supply interruption to the HDD when the transition occurs because the 5v power rail on the Pi is stable. Of course, you'll have to ensure the 5v power rail on the Pi has sufficient current available to power the boost converter/HDD during normal operation. This will require some testing & measurements to validate.