The difference is quite clear: you omit 'есть', when this word is not what you underline in your message! That means that omitting does not give you absolutely the same sentences, so you not 'can', but 'do' omit 'есть' when whis should be done. 

Every school student knows what is the subject and what is the predicate in the sentence. 'есть' is a verb, so it is always a predicate. Predicate contains the core idea of the sentence subject. But what happens, when you omit the predicate? Yes, other words try to take it's role.

Just compare:

> 'В деревне **_один_** новый дом' = 'A **_single_** new house is in the village' = 'The new house is single in the village'

vs

> 'В деревне **_есть_** один новый дом' = 'A new house **_is_** in the village' = 'A new house can be found in the village'

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> 'Здесь **_одно_** место' = '**_One_** place is here' = 'The place here is the only one'
vs

> 'Здесь **_есть_** одно место' = 'There **_is_** one place' = 'A place is here'

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> 'В квартире **_большая_** комната' = 'The room in the flat is **_big_**'

vs

> 'В квартире **_есть_** большая комната' = 'A big room **_is_** in the flat'

Your sentences contained 'только', which is a possible signal to omit 'есть'.

While explaining I noticed, that 'есть' was omitted in sentences, where 'the' was used in English, while 'a' *was* used with 'есть'. That corresponds with the role strength of the subjects. May be it will be the most useful hint for you.