Rainbow Youth communications manager Toni Duder said it was good to receive the donation and hoped Mr Garratt had learned his lesson.
"In future it would be good to work together to promote Rainbow Youth and its work in a more positive light."
She said the transgender experience should not be considered a joke, and that making it one only served to make the experience a negative one.
"Jokes shouldn't target transgender people who are already marginalised and over-represented in negative health statistics."
On the company's Facebook page Mr Garratt offered his apologies.
"We apologise to all those who have been offended by our sign. It was very poor judgment on our part."
In an earlier post, he said there was no offence intended.
"It was not our intention to offend any people in the community ... Cait is more then [sic] welcome to stay at my house with my family anytime. I will have a wine or a beer with her quite happily and it would be an honour."
Rebecca Jones, the mother of a 9-year-old transgender boy, was not satisfied and wanted a "face-to-face apology".
"He seems to think a donation is enough. It is not," she said. "I want an apology to my 9-year-old son AND a donation, and the transgender community is behind me on this."
Ms Jones said he was just trying to "save his reputation".
She said earlier Mr Garratt had not seemed to take a complaint made about the billboard seriously and was "quite insulting" to a friend who'd emailed him.
While he said no offence was intended, in an emailed response to the complainant he appeared to brush off the concerns.
"I think you may need to take a look at yourself and relax a bit and not take life so seriously. I was referring to a Santa sack, your sick mind is the problem."
Ms Jones said members of the online support group she ran for members of the LGBT community were not impressed.
"It gives an excuse to others that they are people to be ridiculed."
She said people needed to be aware of how hurtful transphobia was to transgender people.
There's been a mixed response on social media with some taking the opportunity to make light of Ms Jenner, and the transgender community, while others have been quite critical.
Jesse Evenblij said the billboard was "seriously horrible".
"The company should be ashamed. People just have no clue how Caitlyn has literally saved lives by making transgender 'normal'. Young people can look up to Caitlyn and realise they aren't alone."
A number of companies have also expressed their distaste.
Gough TWL said the transgender community was something that should be celebrated.
"We all have workmates and friends from all walks of life and see that as something to celebrate as opposed to what we see here."
Kia Motors NZ said it had contacted Cranium Signage and had been advised the billboard had been removed.
The signage company was no stranger to outspoken billboards, with its image gallery featuring a number of swearwords and controversial images.
One earlier this year made reference to a pair of Christchurch co-workers that had been snapped in a romantic liaison through their office window: "Feeling exposed? Talk to us about window frosting."
Possibly copyright infringement
Gus Hazel, litigation partner at James & Wells, a law firm specialising in intellectual property, said Cranium's billboard could involve copyright infringement.
"If Cranium reproduces the image [without a licence] then yes this would appear to be infringement."
He said while there were the so-called fair use exceptions to copyright infringement, covering things such as reproduction for the sake of review, critique, parody or satire, he didn't think those would apply in this case.
Mr Hazel said cases of parody mostly involved things such as altered songs, with changed words to make an artistic or political point.
"This example does not appear to reach that level," he said.
"It looks like a relatively crude Photoshop job purely for publicity."
He said within the Copyright Act there was also the issue of moral rights.
This gives authors the right to be identified - or not to be identified - as the author of an altered work and to protect against derogatory treatment of a work.
"[If the photographer] alleges that the image has been bastardised and thinks that impacts the integrity of the image or her as a photographer."
He said usually the first step to mitigate damages was for the offending party to take the image down, or to print a correction.
"The Fair Trading Act might also be relevant - if the image was seen as misleading people into thinking Caitlyn Jenner authorised or endorsed it."
Financial payment depended on each individual case - what was likely lost, if anything, or wrongly gained by the alleged infringer.
