Temperature sensor reads higher inside enclosure
The "Particle Photon" board (who makes these goofy names?) consumes 80 mA at 5V, making its power dissipation at 400 mW. This is a pretty substantial power consumption, and the heat must dissipate via build-up of temperature difference between the board and ambient air. If you want your sensor and MCU inside one enclosure, you should find a way to reduce the consumed power.

One way to reduce the power of a MCU is to use aggressive power management, to put the MCU into sleep mode as soon as you can afford, and not wake it up as long as you can. The time sampling for temperature and humidity is likely in several seconds (given thermal mass of typical PCB and enclosure), so there must be plenty of opportunities to exercise deep power saving modes.