Differences between what 3rd party apps show for remaining battery charge and what the iOS shows can only be explained by the developers of the apps you use....
Note that you should routinely calibrate the phone's battery meter by:
1. Charge to full with AC adaptor.
2. Let phone run until it automatically shuts down - not just to low battery warning.
3. Recharge fully.
When i have battery % turned on, sometimes when i charge it gets stuck at 98 or 99.... I've recharged my battery from a complete drain, meaning the phone goes off completely. I have not seen any differences, and from my knowledge i do not see Apple saying i have to calibrate my battery??? although from dealing with betteries i know what you are talking about...
i do not see Apple saying i have to calibrate my battery???
Even though they don't refer to it as such, they do recommend at least 1 full charge cycle per month:
"Use iPhone Regularly
For proper maintenance of a lithium-based battery, it’s important to keep the electrons in it moving occasionally. Be sure to go through at least one charge cycle per month (charging the battery to 100% and then completely running it down)."
The "keep the electrons moving occasionally" is silly nonsense and not the reason Li batteries respond to full charge cycles - it's actually calibrating the meter and sensors. Li battery age and the calibrations changes over time, which is why this should be done monthly.