以下のパラメータでy軸を無理やり合わせてみましたが、どうですかね?
<option name="charting.axisLabelsY.majorUnit">100</option>
<option name="charting.axisY.maximumNumber">1000</option>
<option name="charting.axisY.minimumNumber">0</option>
<option name="charting.axisLabelsY2.majorUnit">100</option>
<option name="charting.axisY2.maximumNumber">1000</option>
<option name="charting.axisY2.minimumNumber">0</option>
<dashboard>
<label>今日のChart</label>
<row>
<chart>
<searchString>
sourcetype=* | timechart span=1h count by host
| join _time [|search sourcetype=access_* host=apache1* | timechart span=1h count | streamstats window=5 sum(count) as cpu | eval cpu=abs(cpu-1800)/20 | fields - count | rename cpu as cpu_apache1 ]
| join _time [|search sourcetype=access_* host=apache2* | timechart span=1h count | streamstats window=5 sum(count) as cpu | eval cpu=abs(cpu-1800)/20 | fields - count | rename cpu as cpu_apache2 ]
| join _time [|search sourcetype=access_* host=apache3* | timechart span=1h count | streamstats window=5 sum(count) as cpu | eval cpu=abs(cpu-1800)/20 | fields - count | rename cpu as cpu_apache3 ]
| join _time [|search sourcetype=access_* host=* | timechart span=1h count | streamstats window=5 sum(count) as cpu | eval cpu=abs(cpu-1000)/20 | fields - count | rename cpu as cpu_mysql ]
| table _time apache* mysql* cpu*
</searchString>
<title>こんなチャート</title>
<option name="charting.transparentBrushPalette">solidFill</option>
<option name="charting.transparentBrushPalette.colorPalette">@colorPalette</option>
<option name="charting.transparentBrushPalette.alpha">0.7</option>
<option name="charting.data1">view</option>
<option name="charting.data1.table">@data</option>
<option name="charting.data1.columns">[0,1,2,3,4]</option>
<option name="charting.chart.data">@data1</option>
<option name="charting.data2">view</option>
<option name="charting.data2.table">@data</option>
<option name="charting.data2.columns">[0,5,6,7,8]</option>
<option name="charting.chart2.data">@data2</option>
<option name="charting.axisY2">#axisY</option>
<option name="charting.axisLabelsY2">#axisLabelsY</option>
<option name="charting.axisLabelsY2.axis">@axisY2</option>
<option name="charting.chart">area</option>
<option name="charting.chart.columnBrushPalette">@transparentBrushPalette</option>
<option name="charting.chart.stackMode">stacked</option>
<option name="charting.chart.useAbsoluteSpacing">True</option>
<option name="charting.chart.columnSpacing">20</option>
<option name="charting.chart.columnAlignment">.5</option>
<option name="charting.axisTitleY.text">event count (件)</option>
<option name="charting.axisLabelsY.placement">left</option>
<option name="charting.axisLabelsY.majorUnit">100</option>
<option name="charting.axisY.maximumNumber">1000</option>
<option name="charting.axisY.minimumNumber">0</option>
<option name="charting.chart2">line</option>
<option name="charting.chart2.nullValueMode">zero</option>
<option name="charting.chart2.axisY">@axisY2</option>
<option name="charting.axisTitleY2">axisTitle</option>
<option name="charting.axisTitleY2.text">cpu (%)</option>
<option name="charting.axisLabelsY2.placement">right</option>
<option name="charting.axisLabelsY2.majorUnit">100</option>
<option name="charting.axisY2.maximumNumber">1000</option>
<option name="charting.axisY2.minimumNumber">0</option>
<option name="charting.layout.charts">[@chart,@chart2]</option>
<option name="charting.layout.axisLabels">[@axisLabelsX,@axisLabelsY,@axisLabelsY2]</option>
<option name="charting.layout.axisTitles">[@axisTitleX,@axisTitleY,@axisTitleY2]</option>
<option name="charting.legend.placement">bottom</option>
</chart>
</row>
</dashboard>
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