Using a voltage source and limiting current with a resistor causes two things far from optimal:
* Efficiency is limited to 50%. 50% of energy is lost in the resistors - your explicit resistor and the ESR of the capacitor.
* Charging current tapers off, you have highest current in the beginning. Last few percent takes the most time.
Build a current source. I.e., the boost converter must measure and regulate current instead of voltage. Voltage will be just a stopping (end-of-charge) limit. This way
* Efficiency theoretical maximum becomes 100%. Energy is of course still lost in the ESR of the capacitor, and in the resistances of the boost converter itself
* Charging current can be a constant value until stopped, or it can be a CC-CV curve, i.e. constant at first then taper off near the end; in any case with the same peak current, you get much shorter charging time because you can maintain this peak current.
Capacitors have specified maximum current, though. With a current source, it's trivial to ensure it's not exceeded.
Too much current causes too much heating internal to the capacitor.
Often capacitor datasheets specify ripple current for example at 120Hz or 100kHz. This means continuous, repetitive charging and discharging at that frequency, day in day out, resulting in millions of cycles quickly. Obviously if you only charge it a handful of times, the current the capacitor can take undamaged will be much higher than the ripple current rating. But sadly this value is seldom available.
Usually electrolytic capacitors are designed to be fine when connected to an unlimited-current voltage source below the maximum rated voltage of the cap, for some sane number of cycles (hunderds; not millions).
Now how to build a current source? Actually, all proper boost ICs already have some sort of current limit. See the values listed in datasheets. They are not accurate limiters, but it's better than nothing. Make sure the IC doesn't enter some fault/hickup mode with large capacitances, though. It can be quite a chore to find a DC/DC IC which specified unlimited operation against the current limit.