@Sleziak, I definitely agree that this has been a tricky issue for quite some time.
I really like these Pololu 3.3V/0.5A buck/boost regulators that I've been using for a while:
The trouble is, those do not provide in-line charging capability, as @peekay123 said, you'll have to yank the JST connectors out just to charge the battery. I think the Sparkfun boards are perfect for prototyping, but I too do not like their size when you have to cram them into tiny spaces. Even providing us with the option to solder our own choice of lower-profile headers would have helped.
I also wonder: when will we see the final design of the Particle Power Shield?
From the posts, they look similar to the Sparkfun variants, but might have support for solar trickle charging?
The one other solution is to consider the Powerboost 500C from adafruit. (and it's bigger sibling, the 1000C. You don't need to solder the USB jack on (they don't come soldered on); but since they provide +5V output, you'll have to connect to VIN instead of 3V3. This for me is the most compact solution I have come across, as you can lay out the boards end to end and get a lower profile (6-7mm height).
That said, it's an annoying (not to mention inefficient) method to connect power – with the 3.2-4.2V LiPo boosted to 5V, then bucked back to 3.3V on the Photon's onboard regulator. But if you want convenient LiPo charging integrated on your board, this seems to be the only way I can find so far and it's worked for me.