The important point to remember here is that this decision only affects the multiplier on the encounter to determine how difficult it is. Therefore the points to note are:
- This is a "rule of thumb" calculation in the first place. A "Hard" encounter is a very broad area and (despite what the table with its hard boundary suggests) it merges into "Moderate" at one end and "Deadly" at the other.
- It has no impact on the XP the PCs gain in the encounter.
- It is primarily a decision about encounter "pacing" or how many encounters the PCs have before needing to rest. You have way more direct control over this by e.g. bringing an encounter forward if the PCs are flush or deferring one if they are lean on resources.
Therefore it is primarily a judgement call that does not have huge implications. To illustrate consider the examples that you have given:
CR3 Mummy plus (3) CR 1/2 Swarms of Beetles
XP = 700 + 3 x 100 = 1000
Multiplier: 1 or 2 giving 1000 or 2000
CR3 Goblin plus CR1 Lieutenant plus (5) CR 1/4 Swarms of Beetles
XP = 700 + 200 + 5 x 50 = 1050
Multiplier: 1 or 1.5 or 2.5 giving 1050 or 1575 or 2625.
Against say 4 Level 3 PCs, in both cases the first multiplier rates this as "Hard" and any of the others are "Deadly" - what this says is that these are dangerous encounters; be careful. The low CR creatures will have a significant impact on the fight. So using them in the multiplier is reasonable because they low CR creatures will use up significantly more of the party's resources.
Against say 4 level 6 PCs, they are "Easy" to "Medium"; but the low CR creatures will probably be rendered hors de combat in Round 1 - their only contribution is to distract the PCs for that round and maybe burn a fireball. Not using the multiplier would be reasonable here because said fireball will probably be damaging the main protagonist as well so there is no additional drain on party resources.
CR10 and CR1
XP = 5900 + 200 = 6100
Multiplier: 1 or 1.5 giving 6100 or 9150.
This is a deadly encounter for the parties above with the first guy alone (and a probable TPK for the L3 guys).
For 4 level 10 PCs its "Medium" without the multiplier and "Hard" with it. However, given that the CR1 monster can probably be dropped with a Cantrip (3d10), Single attack or at most a 1st level spell (Sleep) it doesn't really add to the difficulty - he will distract 1 of the 4 PCs for part of 1 round. Ignore it.