they can't meaningfully adjust the optics at the source to counter the atmospheric effects.
Actually they can and it's old technology. They use an "aiming" laser and then record the distortion of the reflected signal. It was first created for telescopes to compensate for atmospheric distortion. Between beam steering and this, it's a gimme.
EDIT: found the entry .
Yes. Everything in the atmosphere reflects the signal back. It's simply varying degrees of signal to noise. They've had this technology for decades.
random video: https://www.youtube.com/watch?v=_7TWAJ_bnhM
Now keep in mind, technically they could focus after they fire if the duration is longer than transit time. In turn using the weapon's reflection as the corrective signal. And if it's a pulse weapon, they can always use a modified signal from previous pulses. In addition to the fact that plasma is frequently created by this class of weapon which significantly reduces scatter and reflection.
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