When trainng indoor workouts is it best to use the auto generated magic buckets session or one of the recommended ones that are suggested?
If you achieve the XSS targets, it doesn’t matter. Pick which method works best for you. Switch it up if you wish. 
It’s a common dilemma, but the “Magic Waypoints” or buckets are usually more about hitting those specific strain targets than following a strict script. If you’re feeling fresh and want a bit more structure, the suggested workouts are great, but the buckets give you that extra flexibility to ride how you feel that day. Sometimes just letting the adaptive nature of the system do its thing without overthinking the specific workout name leads to better recovery anyway. Have you noticed a big difference in your “Freshness” status when you stick strictly to the suggestions versus just hitting the target strain manually?
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Pick the option you like best on any particular day. The strain goal is the same.
- A: Select one of the recommended workouts; ERG control on EBC.
- B: Workout generated by Magic Buckets tab or Autogen; ERG control on EBC.
- C: Magic Buckets guided workout; no workout selected.
- D: A + C; start a recommended workout, not up to the task, switch to Slope and finish with XMB. [Possible with EBC Android or when dual recording with Garmin XMB.]
- E: On LIT days you can simply free ride at preferred endurance pace for X minutes to fill Low bucket; no workout selected.
Xert: The freedom to ride! Any which way you want. 
Would the training effect of doing the Magic Buckets intervals (i.e. 40 intervals at 450w for 20 seconds recently prescribed for my workout) with several minutes of rest between them over the course of a few hours be different than doing them as 4 sets of 40/20s? It seems like shorter vs longer recovery would change the training outcome.