Word order

[sonu_gmat]

.....application of commercial fertilizer and irrigation that are required by.....
In this sentence, as per OG, irrigation can be misread as 'application of irrigation'

.....irrigation and application of commercial fertilizer that are required by.....
As per OG, this is correct construction.

Application of X and Y - it could be interpreted as application of X and Y both. Logically application of irrigation is meaningless
X & Y of commercial fertilizer - could it mean both X and Y of CF eventhough there is no meaning for X of CF.

I hope I could put my Q properly. Is there any rule?

[esledge]

The general rule is that good parallelism should aid clarity, not hinder it.

Application of X and Y - it could be interpreted as application of X and Y both. Logically application of irrigation is meaningless
X & Y of commercial fertilizer - could it mean both X and Y of CF eventhough there is no meaning for X of CF.

I hope I could put my Q properly. Is there any rule?

I'll write my own examples to avoid copyright issues with the OG. (We suggest that forum users do the same, for future reference.)

MORE confusing: "...application of primer and surface preparation that are required for a good finish..."
Reasons:
(1) You could apply surface preparation, depending on what is meant by that...I guess. I disagree that, in your example, application of irrigation is totally meaningless. It's not an ideal way to say so, but a farmer could install an irrigation system or apply water and call it "application of irrigation." But fertilizer is an inanimate object, while irrigation is a (possibly) intangible noun, so I see the point that they aren't supposed to be parallel.
(2) The modifier that follows, "that are required" uses a plural verb and is clearly meant to modify both nouns (primer and prep), further linking them as two parallel items, two things that are applied.

LESS confusing: "surface preparation and application of primer that are required for a good finish..."
(1) Here, surface preparation and application are not only both nouns, but they are the same type of noun: action noun, a thing someone would do.
(2) The modifier that follows, "that are required" uses a plural verb, which cannot refer to the singular primer, so it is clearly the preparation and application that are required.
(3) Prepositional phrases, such as of primer, do not "distribute back" over a list of parallel things the same way a preposition might "distribute forward" over a list of things.
Janet is a fan of X, Y, and Z. = Janet is a fan of X, of Y, and of Z.
BUT
Larry is afraid of bats, owls, and other creatures of the night. is NOT interpreted as Larry is afraid of bats of the night, owls of the night, and other creatures of the night.