"Agriculture" appears to measure the emissions generated directly from agricultural processes themselves, as well as "secondary" combustion inputs. This includes "enteric fermentation in domestic livestock, livestock manure management, rice cultivation, agricultural soil management, liming, urea fertilization, and field burning of agricultural residues". However, based on my reading -- please correct me if I'm wrong -- large parts of the agricultural process are included in each of the transportation, electricity, and industry categories. Thus the effects of agriculture would be seen downstream and upstream in these other categories. For example, any agricultural use of electricity is included in "electricity", not "agriculture".
An aside on meat specifically: since meat production involves more inputs, such as feed, livestock, and additional processing, you would have to account for these when comparing to a non-meat diet. For example, every cow involves the transportation of the cow, the (industrial) production of fertilizers needed to grow its feed, the production of the materials to package the feed, the transportation of the feed to a facility for packaging, the transportation of the packaged feed to a farm, the transportation of the cow to a slaughtering facility, the refrigeration of the cuts of meat, etc. The emissions generated during these steps would belong to the transportation, industry, and electricity categories, not even counting the extra emissions included in the agriculture category. While all food production would have steps such as these, clearly there are more steps in meat production because there are more inputs.
Now, back to the original point of transportation versus agriculture: the report says that 25% of the transportation category is "freight" -- I believe the shipping I described above would be included in this. However, to your point, around 60% of transportation is due to passenger vehicles and light-duty trucks, which is quite significant and likely mostly personal use (rather than agricultural), and that's where changing transportation methods can make a difference. I'm too tired to find what percent of industry and electricity are related to the agricultural process, but you would need to calculate this and compare it to personal transportation use in order to get a fair comparison.
In my personal opinion, I think we should both reduce meat consumption and personal vehicle use. No need to pick favorites.
https://www.mekkographics.com/meat-consumption-by-country-an...
The United States, China and Brazil produce the most beef:
https://ourworldindata.org/meat-production
In my reading, there is a great inequality in distribution of both consumption and production and if both could be equalized downwards, that would mean a significant reduction overall.
I looked at the document, and it doesn’t seem to include the embedded CO2 from Urea production (fertiliser) which would be a large emission omission. Perhaps it shows up in the detailed breakdown somewhere.
https://ourworldindata.org/food-ghg-emissions
According to the article, 26% of all GHG emissions are from food production.
Of that:
31% of all food production comes from livestock and fisheries.
27% comes from crop production, with 6% for animal feed and 21% for human food.
24% comes from land use, 8% for human food and 16% for livestock.
18% comes from ransport and other emissions from the supply chain.