One significant downside, in addition to AO functionality, to trying to continue using the Jupiter units is changes to the hidden stat that determines move order.
Harpoon Grenadiers (SAJM ranged) have equal initiative to Overclock Orbiters (SAT artillery) - i've been using mass overclock orbiters to take them out in small numbers in SAJM GBG quite cleanly. Pressurizers (SAT ranged) have higher initiative (and thus always move before the artillery and do significant damage - noted from PvP arena bots). But as long as there's no artillery, contact + rogue advantage is likely to make grenadiers still a valuable tool.
Permafrost Drones (SAT fast) also have higher initiative than Abyssal Gliders (SAJM fast) - and thus any 8 abyssal glider comps will take initial hits from any permafrost drones on defense. 8 Abyssal Gliders may be better than 8 Permafrost Drones against a defending army with no Permafrost Drones though - but there's generally a better attack against such an army: Overclock Orbiters (SAT Artillery).
That said, that doesn't mean their SAT counterparts are great - the reduced range of the fast and the no-contact on the ranged does make them less powerful than the SAJM experience.
The powerful unit this time is the Overclock Orbiter - but it has a strong counter (flying Permafrost Drones) and a weak counter (ranged Pressurizer that moves before the orbiters and can often hit them first) so you can't use it all the time.
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If you're insist on fast autobattling it seems likely that defense for attacking army will be more important than ever in this age as you'll want to minimize the damage taken by units that all have downsides that make them less than perfect. Permafrost Drones are probably the most general unit - and if coupled with good defense (read: at least 50% higher than your attack, if not more) are usable against everything. Without good defense, you're probably going to be taking a lot more losses due to their imperfections.
But this is also an age that rewards changing your army depending on the composition of the defense. Fitting in Overclock Orbiters wherever they work well enough will push your attrition way higher than resting on one solid army.